Data from: DNA and RNA-sequence based GWAS highlights membrane-transport genes as key modulators of milk lactose content

Lopdell TJ, Tiplady K, Struchalin M, Johnson TJJ, Keehan M, Sherlock R, Couldrey C, Davis SR, Snell RG, Spelman RJ, Littlejohn MD

Date Published: December 15, 2017

DOI: https://doi.org/10.5061/dryad.vv469

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Title LC_GWAS_results.txt
Downloaded 2 times
Description GWAS of lactose concentration in 12k cows, using a generalised least squares model to account for pedigree.
Download LC_GWAS_results.txt.gz (23.56 Mb)
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Title LY_GWAS_results.txt
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Description GWAS of lactose yield in 12k cows, using a generalised least squares model to account for pedigree.
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Title imputed_seq_results_22loci-LC.txt
Downloaded 1 time
Description Associations for 1Mbp windows of imputed whole genome sequence around 5 GWAS peaks for lactose concentration, using GLS to account for pedigree.
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Title imputed_seq_results_5loci-LY.txt
Downloaded 3 times
Description Associations for 1Mbp windows of imputed whole genome sequence around 5 GWAS peaks for lactose yield, using GLS to account for pedigree.
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Title eQTL for genes at lactose QTL peaks
Downloaded 1 time
Description 1Mbp cis-eQTL from imputed whole-genome sequence for 313 genes arounds QTL peaks for lactose phenotypes. Calculated using GLS to account for pedigree.
Download all-eQTL-seq-model-outputs.zip (26.73 Mb)
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Title imputed-seq-genotypes-Chr1.153640000-154640000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr1:153.96 LC QTL, for 357 animals.
Download imputed-seq-genotypes-Chr1.153640000-15464...cf.gz (2.012 Mb)
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Title imputed-seq-genotypes-Chr2.127140000-128140000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr2:127.64 LC QTL, for 357 animals.
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Title imputed-seq-genotypes-Chr3.15020000-16020000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr3:15.52 LC QTL, for 357 animals.
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Title imputed-seq-genotypes-Chr3.53340000-54340000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr3:53.84 LC QTL, for 357 animals.
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Title imputed-seq-genotypes-Chr5.20640000-21640000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr5:21.14 LC QTL, for 357 animals.
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Title imputed-seq-genotypes-Chr5.31060000-32060000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr5:31.56 LC QTL, for 357 animals.
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Title imputed-seq-genotypes-Chr5.43660000-44660000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr5:44.16 LC QTL, for 357 animals.
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Title imputed-seq-genotypes-Chr5.93440000-94440000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr5:93.94 LY QTL, for 357 animals.
Download imputed-seq-genotypes-Chr5.93440000-944400...cf.gz (1.954 Mb)
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Title imputed-seq-genotypes-Chr6.37260000-38260000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr6:37.76 LC QTL, for 357 animals.
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Title imputed-seq-genotypes-Chr6.88540000-89540000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr6:89.04 LC QTL, for 357 animals.
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Title imputed-seq-genotypes-Chr7.8270000-9270000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr7:8.77 LC QTL, for 357 animals.
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Title imputed-seq-genotypes-Chr10.1640000-2640000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr10:2.14 LC QTL, for 357 animals.
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Title imputed-seq-genotypes-Chr11.62950000-63950000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr11:63.45 LY QTL, for 357 animals.
Download imputed-seq-genotypes-Chr11.62950000-63950...cf.gz (1.381 Mb)
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Title imputed-seq-genotypes-Chr14.1270000-2270000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr14:1.77 LY QTL, for 357 animals.
Download imputed-seq-genotypes-Chr14.1270000-2270000.vcf.gz (1.184 Mb)
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Title imputed-seq-genotypes-Chr15.27860000-28860000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr15:28.36 LC QTL, for 357 animals.
Download imputed-seq-genotypes-Chr15.27860000-28860...cf.gz (1.095 Mb)
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Title imputed-seq-genotypes-Chr16.24490000-25490000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr16:24.99 LC QTL, for 357 animals.
Download imputed-seq-genotypes-Chr16.24490000-25490...cf.gz (1.360 Mb)
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Title imputed-seq-genotypes-Chr16.67270000-68270000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr16:67.77 LC QTL, for 357 animals.
Download imputed-seq-genotypes-Chr16.67270000-68270...cf.gz (1.179 Mb)
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Title imputed-seq-genotypes-Chr17.55970000-56970000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr17:56.47 LC QTL, for 357 animals.
Download imputed-seq-genotypes-Chr17.55970000-56970...cf.gz (743.4 Kb)
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Title imputed-seq-genotypes-Chr19.33010000-34010000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr19:33.51 LC QTL, for 357 animals.
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Title imputed-seq-genotypes-Chr19.42490000-43490000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr19:42.99 LC QTL, for 357 animals.
Download imputed-seq-genotypes-Chr19.42490000-43490...cf.gz (917.1 Kb)
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Title imputed-seq-genotypes-Chr19.60630000-61630000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr19:61.13 LC QTL, for 357 animals.
Download imputed-seq-genotypes-Chr19.60630000-61630...cf.gz (1.535 Mb)
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Title imputed-seq-genotypes-Chr20.31190000-32190000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr20:31.69 LY QTL, for 357 animals.
Download imputed-seq-genotypes-Chr20.31190000-32190...cf.gz (1.191 Mb)
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Title imputed-seq-genotypes-Chr20.57950000-58950000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr20:58.45 LC QTL, for 357 animals.
Download imputed-seq-genotypes-Chr20.57950000-58950...cf.gz (1.797 Mb)
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Title imputed-seq-genotypes-Chr26.22460000-23460000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr26:22.96 LY QTL, for 357 animals.
Download imputed-seq-genotypes-Chr26.22460000-23460...cf.gz (1.712 Mb)
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Title imputed-seq-genotypes-Chr27.35710000-36710000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr27:36.21 LC QTL, for 357 animals.
Download imputed-seq-genotypes-Chr27.35710000-36710...cf.gz (1.473 Mb)
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Title imputed-seq-genotypes-Chr28.6060000-7060000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr28:6.56 LC QTL, for 357 animals.
Download imputed-seq-genotypes-Chr28.6060000-7060000.vcf.gz (2.273 Mb)
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Title imputed-seq-genotypes-Chr29.9110000-10110000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr29:9.61 LC QTL, for 357 animals.
Download imputed-seq-genotypes-Chr29.9110000-101100...cf.gz (1.547 Mb)
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Title imputed-seq-genotypes-12k-Chr1.153640000-154640000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr1:154.14 LC QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr1.153640000-15464...cf.gz (72.07 Mb)
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Title imputed-seq-genotypes-12k-Chr2.127140000-128140000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr2:127.64 LC QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr2.127140000-12814...cf.gz (44.09 Mb)
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Title imputed-seq-genotypes-12k-Chr3.15020000-16020000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr3:15.52 LC QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr3.15020000-160200...cf.gz (43.35 Mb)
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Title imputed-seq-genotypes-12k-Chr3.53340000-54340000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr3:53.84 LC QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr3.53340000-543400...cf.gz (78.42 Mb)
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Title imputed-seq-genotypes-12k-Chr5.20640000-21640000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr5:21.14 LC QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr5.20640000-216400...cf.gz (59.90 Mb)
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Title imputed-seq-genotypes-12k-Chr5.31060000-32060000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr5:31.56 LC QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr5.31060000-320600...cf.gz (56.45 Mb)
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Title imputed-seq-genotypes-12k-Chr5.43660000-44660000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr5:44.16 LC QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr5.43660000-446600...cf.gz (50.55 Mb)
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Title imputed-seq-genotypes-12k-Chr5.93440000-94440000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr5:93.94 LY QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr5.93440000-944400...cf.gz (77.22 Mb)
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Title imputed-seq-genotypes-12k-Chr6.37260000-38260000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr6:37.76 LC QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr6.37260000-382600...cf.gz (47.00 Mb)
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Title imputed-seq-genotypes-12k-Chr6.88540000-89540000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr3:89.04 LC QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr6.88540000-895400...cf.gz (82.22 Mb)
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Title imputed-seq-genotypes-12k-Chr7.8270000-9270000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr7:8.77 LC QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr7.8270000-9270000.vcf.gz (44.30 Mb)
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Title imputed-seq-genotypes-12k-Chr10.1640000-2640000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr10:2.14 LC QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr10.1640000-2640000.vcf.gz (80.80 Mb)
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Title imputed-seq-genotypes-12k-Chr11.62950000-63950000.vcf
Downloaded 1 time
Description Imputed genotypes for variants within 1Mbp of the Chr11:63.45 LY QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr11.62950000-63950...cf.gz (46.49 Mb)
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Title imputed-seq-genotypes-Chr14.1270000-2270000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr14:1.77 LY QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr14.1270000-2270000.vcf.gz (42.34 Mb)
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Title imputed-seq-genotypes-12k-Chr15.27860000-28860000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr15:28.36 LC QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr15.27860000-28860...cf.gz (39.67 Mb)
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Title imputed-seq-genotypes-12k-Chr16.24490000-25490000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr16:24.99 LC QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr16.24490000-25490...cf.gz (51.45 Mb)
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Title imputed-seq-genotypes-12k-Chr16.67270000-68270000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr16:67.77 LC QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr16.67270000-68270...cf.gz (45.45 Mb)
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Title imputed-seq-genotypes-12k-Chr17.55970000-56970000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr17:56.47 LC QTL, for 12,000 animals.
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Title imputed-seq-genotypes-12k-Chr19.33010000-34010000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr19:33.51 LC QTL, for 12,000 animals.
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Title imputed-seq-genotypes-12k-Chr19.42490000-43490000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr19:42.99 LC QTL, for 12,000 animals.
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Title imputed-seq-genotypes-12k-Chr19.60630000-61630000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr19:61.13 LC QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr19.60630000-61630...cf.gz (65.10 Mb)
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Title imputed-seq-genotypes-12k-Chr20.31190000-32190000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr20:31.69 LY QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr20.31190000-32190...cf.gz (45.47 Mb)
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Title imputed-seq-genotypes-12k-Chr20.57950000-58950000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr20:58.45 LC QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr20.57950000-58950...cf.gz (69.39 Mb)
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Title imputed-seq-genotypes-Chr26.22460000-23460000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr26:22.96 LY QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr26.22460000-23460...cf.gz (64.81 Mb)
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Title imputed-seq-genotypes-12k-Chr27.35710000-36710000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr27:36.21 LC QTL, for 12,000 animals.
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Title imputed-seq-genotypes-12k-Chr28.6060000-7060000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr28:6.56 LC QTL, for 12,000 animals.
Download imputed-seq-genotypes-Chr28.6060000-7060000.vcf.gz (89.66 Mb)
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Title imputed-seq-genotypes-12k-Chr29.9110000-10110000.vcf
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Description Imputed genotypes for variants within 1Mbp of the Chr29:9.61 LC QTL, for 12,000 animals.
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Title HD-and-RNA-variants-Chr1.vcf
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Description All HD and RNAseq variants on chromosome 1. Used in the paper for LC and LY GWAS.
Download chr1.vcf.gz (304.2 Mb)
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Title HD-and-RNA-variants-Chr2.vcf
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Description All HD and RNAseq variants on chromosome 2. Used in the paper for LC and LY GWAS.
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Title HD-and-RNA-variants-Chr3.vcf
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Description All HD and RNAseq variants on chromosome 3. Used in the paper for LC and LY GWAS.
Download chr3.vcf.gz (265.4 Mb)
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Title HD-and-RNA-variants-Chr4.vcf
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Description All HD and RNAseq variants on chromosome 4. Used in the paper for LC and LY GWAS.
Download chr4.vcf.gz (240.5 Mb)
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Title HD-and-RNA-variants-Chr5.vcf
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Description All HD and RNAseq variants on chromosome 5. Used in the paper for LC and LY GWAS.
Download chr5.vcf.gz (252.0 Mb)
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Title HD-and-RNA-variants-Chr6.vcf
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Description All HD and RNAseq variants on chromosome 6. Used in the paper for LC and LY GWAS.
Download chr6.vcf.gz (233.3 Mb)
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Title HD-and-RNA-variants-Chr7.vcf
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Description All HD and RNAseq variants on chromosome 7. Used in the paper for LC and LY GWAS.
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Title HD-and-RNA-variants-Chr8.vcf
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Description All HD and RNAseq variants on chromosome 8. Used in the paper for LC and LY GWAS.
Download chr8.vcf.gz (190.1 Mb)
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Title HD-and-RNA-variants-Chr9.vcf
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Description All HD and RNAseq variants on chromosome 9. Used in the paper for LC and LY GWAS.
Download chr9.vcf.gz (196.7 Mb)
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Title HD-and-RNA-variants-Chr10.vcf
Downloaded 1 time
Description All HD and RNAseq variants on chromosome 10. Used in the paper for LC and LY GWAS.
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Title HD-and-RNA-variants-Chr11.vcf
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Description All HD and RNAseq variants on chromosome 11. Used in the paper for LC and LY GWAS.
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Title HD-and-RNA-variants-Chr12.vcf
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Description All HD and RNAseq variants on chromosome 12. Used in the paper for LC and LY GWAS.
Download chr12.vcf.gz (151.6 Mb)
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Title HD-and-RNA-variants-Chr13.vcf
Downloaded 1 time
Description All HD and RNAseq variants on chromosome 13. Used in the paper for LC and LY GWAS.
Download chr13.vcf.gz (158.7 Mb)
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Title HD-and-RNA-variants-Chr14.vcf
Downloaded 1 time
Description All HD and RNAseq variants on chromosome 14. Used in the paper for LC and LY GWAS.
Download chr14.vcf.gz (152.2 Mb)
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Title HD-and-RNA-variants-Chr15.vcf
Downloaded 1 time
Description All HD and RNAseq variants on chromosome 15. Used in the paper for LC and LY GWAS.
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Title HD-and-RNA-variants-Chr16.vcf
Description All HD and RNAseq variants on chromosome 16. Used in the paper for LC and LY GWAS.
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Title HD-and-RNA-variants-Chr17.vcf
Downloaded 1 time
Description All HD and RNAseq variants on chromosome 17. Used in the paper for LC and LY GWAS.
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Title HD-and-RNA-variants-Chr18.vcf
Downloaded 1 time
Description All HD and RNAseq variants on chromosome 18. Used in the paper for LC and LY GWAS.
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Title HD-and-RNA-variants-Chr19.vcf
Downloaded 1 time
Description All HD and RNAseq variants on chromosome 19. Used in the paper for LC and LY GWAS.
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Title HD-and-RNA-variants-Chr20.vcf
Downloaded 1 time
Description All HD and RNAseq variants on chromosome 20. Used in the paper for LC and LY GWAS.
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Title HD-and-RNA-variants-Chr21.vcf
Downloaded 1 time
Description All HD and RNAseq variants on chromosome 21. Used in the paper for LC and LY GWAS.
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Title HD-and-RNA-variants-Chr22.vcf
Downloaded 1 time
Description All HD and RNAseq variants on chromosome 22. Used in the paper for LC and LY GWAS.
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Title HD-and-RNA-variants-Chr23.vcf
Downloaded 1 time
Description All HD and RNAseq variants on chromosome 23. Used in the paper for LC and LY GWAS.
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Title HD-and-RNA-variants-Chr24.vcf
Downloaded 1 time
Description All HD and RNAseq variants on chromosome 24. Used in the paper for LC and LY GWAS.
Download chr24.vcf.gz (109.2 Mb)
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Title HD-and-RNA-variants-Chr25.vcf
Downloaded 1 time
Description All HD and RNAseq variants on chromosome 25. Used in the paper for LC and LY GWAS.
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Title HD-and-RNA-variants-Chr26.vcf
Downloaded 1 time
Description All HD and RNAseq variants on chromosome 26. Used in the paper for LC and LY GWAS.
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Title HD-and-RNA-variants-Chr27.vcf
Downloaded 1 time
Description All HD and RNAseq variants on chromosome 27. Used in the paper for LC and LY GWAS.
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Title HD-and-RNA-variants-Chr28.vcf
Downloaded 1 time
Description All HD and RNAseq variants on chromosome 28. Used in the paper for LC and LY GWAS.
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Title HD-and-RNA-variants-Chr29.vcf
Downloaded 1 time
Description All HD and RNAseq variants on chromosome 29. Used in the paper for LC and LY GWAS.
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Title validation-genotypes-lc.vcf
Downloaded 1 time
Description Genotypes of the 22 tag SNPs for the LC phenotype QLT peaks in the 18k validation animals.
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Title validation-genotypes-ly.vcf
Downloaded 1 time
Description Genotypes of the 5 tag SNPs for the LY phenotype QLT peaks in the 18k validation animals.
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Title validation_results_LC
Downloaded 1 time
Description The association statistics for the 22 LC QTL peaks in the 18k animal validation set.
Download lcts_pct_htdat_adj_cgrp_brd.validation.txt (1.246 Kb)
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Title validation_results_LY
Downloaded 1 time
Description The association statistics for the 5 LY QTL peaks in the 18k animal validation set.
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Title README file
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Description A description of what all the other files contain.
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When using this data, please cite the original publication:

Lopdell TJ, Tiplady K, Struchalin M, Johnson TJJ, Keehan M, Sherlock R, Couldrey C, Davis SR, Snell RG, Spelman RJ, Littlejohn MD (2017) DNA and RNA-sequence based GWAS highlights membrane-transport genes as key modulators of milk lactose content. BMC Genomics 18: 968. https://doi.org/10.1186/s12864-017-4320-3

Additionally, please cite the Dryad data package:

Lopdell TJ, Tiplady K, Struchalin M, Johnson TJJ, Keehan M, Sherlock R, Couldrey C, Davis SR, Snell RG, Spelman RJ, Littlejohn MD (2017) Data from: DNA and RNA-sequence based GWAS highlights membrane-transport genes as key modulators of milk lactose content. Dryad Digital Repository. https://doi.org/10.5061/dryad.vv469
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