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b486381ac2e475381e8184b2c7c165e4 ./AFR.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz |
f9daa2144063c327006e4cffcae21510 ./AMR.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz |
6162a93cb80935168c0bfa519748b054 ./EAS.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz |
2c78cb84cb1f90b576510decc45e5b9b ./EUR.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz |
8f9eca55f9fc25e2a58a013a1ae0a9af ./PAN.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz |
fdf1c9831d74ae8e9c3960865cf7c22c ./SAS.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz |
f1e0657ee7549915e5bde2f6324b0e57 ./AFR.ALL.split_norm_af.1kg_30x.hg38.vcf.gz |
f4109fc1e23c0eb62762caaf4bed24d5 ./AMR.ALL.split_norm_af.1kg_30x.hg38.vcf.gz |
5360451ef7f31cb44471144e427e6cfe ./EAS.ALL.split_norm_af.1kg_30x.hg38.vcf.gz |
9e1aa56d8b843fef724b67e23932c95b ./EUR.ALL.split_norm_af.1kg_30x.hg38.vcf.gz |
32e160c40d5463befff35ab6e1310349 ./PAN.ALL.split_norm_af.1kg_30x.hg38.vcf.gz |
59fbbf0f30a7ad2f13a04b035e5dc373 ./SAS.ALL.split_norm_af.1kg_30x.hg38.vcf.gz |
SNP CHR POS REF ALT Frq BETA SE P Dir HetP N |
1:725932_G_A 1 725932 A G 0.0040 -0.0737 0.1394 0.597 -?+- 0.4502 166718 |
1:725933_A_G 1 725933 A G 0.9960 0.0737 0.1394 0.5973 +?-+ 0.4505 166718 |
1:737801_T_C 1 737801 T C 0.9949 0.0490 0.1231 0.6908 +?-+ 0.4599 166718 |
1:749963_T_TAA 1 749963 T TAA 0.1626 0.0213 0.0199 0.2846 -?++ 0.32 166718 |
1:751343_T_A 1 751343 A T 0.1407 0.0172 0.0156 0.2705 -?++ 0.3884 166718 |
1:751488_G_GA 1 751488 G GA 0.8530 -0.0187 0.0174 0.283 +?-- 0.3859 166718 |
1:751756_T_C 1 751756 T C 0.8600 -0.0172 0.0156 0.2705 +?-- 0.3884 166718 |
1:752566_G_A 1 752566 A G 0.8422 -0.0155 0.0131 0.235 +?-- 0.4375 166718 |
1:752721_A_G 1 752721 A G 0.2507 0.0204 0.0147 0.165 -?++ 0.4151 166718 |
1:752894_T_C 1 752894 T C 0.1440 0.0169 0.0147 0.2525 -?++ 0.402 166718 |
1:753405_C_A 1 753405 A C 0.8570 -0.0169 0.0148 0.2539 +?-- 0.3917 166718 |
1:753425_T_C 1 753425 T C 0.1443 0.0171 0.0148 0.2478 -?++ 0.4051 166718 |
1:753474_C_G 1 753474 C G 0.2977 0.0209 0.0157 0.1815 -?++ 0.423 166718 |
1:753541_G_A 1 753541 A G 0.2431 0.0248 0.0182 0.1729 -?++ 0.3755 166718 |
1:754182_A_G 1 754182 A G 0.2505 0.0222 0.0166 0.1817 -?++ 0.4077 166718 |
1:754192_A_G 1 754192 A G 0.2505 0.0222 0.0166 0.1817 -?++ 0.4077 166718 |
1:754334_T_C 1 754334 T C 0.2373 0.0253 0.0165 0.1267 -?++ 0.3599 166718 |
1:754503_G_A 1 754503 A G 0.7499 -0.0235 0.0157 0.1336 +?-- 0.3875 166718 |
1:754964_C_T 1 754964 T C 0.7488 -0.0235 0.0157 0.1336 +?-- 0.3875 166718 |
1:755890_A_T 1 755890 A T 0.1439 0.0173 0.0156 0.2677 -?++ 0.4029 166718 |
1:756268_G_A 1 756268 A G 0.7672 -0.0219 0.0174 0.2075 +?-- 0.4101 166718 |
1:756434_G_C 1 756434 C G 0.1203 0.0200 0.0190 0.2917 -?++ 0.3262 166718 |
1:756604_A_G 1 756604 A G 0.1464 0.0173 0.0155 0.2663 -?++ 0.4027 166718 |
1:757640_G_A 1 757640 A G 0.7196 -0.0213 0.0173 0.2183 +?-- 0.4236 166718 |
1:757734_C_T 1 757734 T C 0.8533 -0.0173 0.0156 0.2677 +?-- 0.4029 166718 |
1:757843_C_A 1 757843 A C 0.7519 -0.0179 0.0157 0.2527 +?-- 0.4168 166718 |
1:757936_C_A 1 757936 A C 0.8538 -0.0172 0.0156 0.2705 +?-- 0.3884 166718 |
1:758144_A_G 1 758144 A G 0.1512 0.0171 0.0148 0.2478 -?++ 0.4051 166718 |
1:758626_C_T 1 758626 T C 0.8546 -0.0173 0.0157 0.2689 +?-- 0.393 166718 |
1:759293_T_A 1 759293 A T 0.1027 0.0226 0.0217 0.2964 -?++ 0.2973 166718 |
1:759837_T_A 1 759837 A T 0.8544 -0.0182 0.0157 0.246 +?-- 0.3793 166718 |
1:760912_C_T 1 760912 T C 0.8425 -0.0171 0.0148 0.248 +?-- 0.3874 166718 |
1:761147_T_C 1 761147 T C 0.1581 0.0171 0.0148 0.248 -?++ 0.3874 166718 |
1:761732_C_T 1 761732 T C 0.7057 -0.0244 0.0175 0.1632 +?-- 0.4087 166718 |
1:761752_C_T 1 761752 T C 0.8506 -0.0180 0.0157 0.2505 +?-- 0.3668 166718 |
1:762273_G_A 1 762273 A G 0.8390 -0.0176 0.0165 0.2869 +?-- 0.4411 166718 |
1:762485_C_A 1 762485 A C 0.1036 0.0227 0.0225 0.3127 -?++ 0.3527 166718 |
1:762589_G_C 1 762589 C G 0.8522 -0.0172 0.0165 0.2977 +?-- 0.416 166718 |
1:762592_C_G 1 762592 C G 0.1479 0.0173 0.0165 0.2957 -?++ 0.4146 166718 |
1:762601_T_C 1 762601 T C 0.1479 0.0173 0.0165 0.2957 -?++ 0.4146 166718 |
1:762632_T_A 1 762632 A T 0.8524 -0.0173 0.0165 0.2957 +?-- 0.4146 166718 |
1:763394_G_A 1 763394 A G 0.7023 -0.0258 0.0183 0.1579 +?-- 0.473 166718 |
1:764191_T_G 1 764191 T G 0.8648 -0.0178 0.0181 0.3256 +?-- 0.3988 166718 |
1:766007_A_C 1 766007 A C 0.9234 -0.0228 0.0302 0.4506 +?-- 0.2594 166718 |
1:769138_CAT_C 1 769138 CAT C 0.8550 -0.0189 0.0183 0.3013 +?-- 0.3827 166718 |
1:769223_C_G 1 769223 C G 0.8740 -0.0199 0.0208 0.338 +?-- 0.3595 166718 |
1:771823_T_C 1 771823 T C 0.1512 0.0180 0.0182 0.3235 -?++ 0.4164 166718 |
1:771967_G_A 1 771967 A G 0.1315 0.0189 0.0207 0.3616 -?++ 0.3908 166718 |
1:772755_A_C 1 772755 A C 0.1496 0.0187 0.0191 0.3281 -?++ 0.4264 166718 |
1:775181_A_G 1 775181 A G 0.8552 -0.0188 0.0199 0.3461 +?-- 0.366 166718 |
1:775659_A_G 1 775659 A G 0.1588 0.0183 0.0190 0.3366 -?++ 0.3855 166718 |
1:777122_A_T 1 777122 A T 0.1573 0.0187 0.0191 0.3272 -?++ 0.3842 166718 |
1:777745_G_A 1 777745 A G 0.0022 0.1153 0.1424 0.4184 -?++ 0.6285 166718 |
1:778745_A_G 1 778745 A G 0.8623 -0.0204 0.0216 0.3463 +?-- 0.3381 166718 |
1:779322_A_G 1 779322 A G 0.8550 -0.0194 0.0208 0.3512 +?-- 0.3647 166718 |
1:780397_C_T 1 780397 T C 0.0252 -0.0278 0.0489 0.5703 -?++ 0.1364 166718 |
1:783318_A_G 1 783318 A G 0.8722 -0.0211 0.0242 0.3838 +?-- 0.303 166718 |
1:786995_G_A 1 786995 A G 0.1460 0.0201 0.0225 0.3725 -?++ 0.3364 166718 |
1:787262_C_G 1 787262 C G 0.1586 0.0189 0.0216 0.3829 -?++ 0.3529 166718 |
1:787606_G_T 1 787606 T G 0.1478 0.0204 0.0218 0.3486 -?++ 0.3223 166718 |
1:789513_GA_G 1 789513 G GA 0.1478 0.0191 0.0225 0.3949 -?++ 0.335 166718 |
1:791191_G_A 1 791191 A G 0.1458 0.0195 0.0234 0.4039 -?++ 0.328 166718 |
1:799276_G_A 1 799276 A G 0.0101 -0.0357 0.0621 0.5651 -?-+ 0.3106 166718 |
1:810458_G_A 1 810458 A G 0.0037 -0.0834 0.1090 0.444 -?-+ 0.4703 166718 |
1:832398_T_C 1 832398 T C 0.1662 0.0047 0.0223 0.8347 -?++ 0.1507 166718 |
1:833927_T_C 1 833927 T C 0.8139 0.0112 0.0215 0.602 +?+- 0.3299 166718 |
1:834198_T_C 1 834198 T C 0.8209 0.0110 0.0215 0.6074 +?+- 0.3349 166718 |
1:834928_A_G 1 834928 A G 0.8094 0.0118 0.0214 0.5814 +?+- 0.3222 166718 |
1:834999_G_A 1 834999 A G 0.1886 -0.0116 0.0214 0.5868 -?-+ 0.3271 166718 |
1:835499_A_G 1 835499 A G 0.7664 0.0197 0.0207 0.3421 +?+- 0.1452 166718 |
1:836529_C_G 1 836529 C G 0.8305 0.0134 0.0207 0.5151 +?+- 0.2539 166718 |
1:836924_G_A 1 836924 A G 0.1690 -0.0133 0.0207 0.5202 -?-+ 0.2585 166718 |
1:837192_A_G 1 837192 A G 0.7050 0.0316 0.0189 0.09419 +?++ 0.2101 166718 |
1:837753_G_A 1 837753 A G 0.0048 0.0985 0.1030 0.3389 +?++ 0.9687 166718 |
1:838094_CA_C 1 838094 CA C 0.9981 0.1594 0.2039 0.4343 +?++ 0.9585 166718 |
1:838329_G_GC 1 838329 G GC 0.8250 0.0085 0.0205 0.6798 +?+- 0.2234 166718 |
1:838387_T_C 1 838387 T C 0.8307 0.0000 0.0206 0.9982 +?+- 0.1159 166718 |
1:838555_C_A 1 838555 A C 0.3817 -0.0148 0.0181 0.4118 -?0+ 0.181 166718 |
1:840327_G_A 1 840327 A G 0.1448 -0.0043 0.0188 0.8185 ---+ 0.1475 191764 |
1:840863_T_A 1 840863 A T 0.0064 -0.2373 0.1151 0.03925 +?-+ 0.3307 166718 |
1:841085_C_G 1 841085 C G 0.5982 0.0224 0.0174 0.1976 +?++ 0.2241 166718 |
1:842013_T_G 1 842013 T G 0.8466 0.0047 0.0185 0.8009 +++- 0.1546 191764 |
1:842057_A_AAACTCAGCTGCCTCTCCCCTTC 1 842057 A AAACTCAGCTGCCTCTCCCCTTC 0.5757 0.0276 0.0174 0.1138 +?++ 0.2231 166718 |
1:842362_C_T 1 842362 T C 0.1744 0.0000 0.0205 0.9998 -?-+ 0.1133 166718 |
1:842446_G_C 1 842446 C G 0.0065 -0.2347 0.1134 0.03851 +?-+ 0.3293 166718 |
1:842685_T_C 1 842685 T C 0.9916 0.0684 0.0945 0.4697 -?+- 0.768 166718 |
1:844324_G_A 1 844324 A G 0.6709 -0.0280 0.0174 0.1083 -?-+ 0.133 166718 |
End of preview. Expand in Data Studio
GWASLab reference datasets
Processed genomic reference files used by GWASLab (download_ref / gwaslab download ref). This dataset replaces the previous Dropbox hosting for GWASLab-processed panels. Official dbSNP VCFs, UCSC FASTA, Ensembl/RefSeq GTF, and liftOver chains stay at their original hosts.
Package catalog: reference.json. Checksums for every file in this repo are in md5sum.txt.
Download with GWASLab
import gwaslab as gl
gl.download_ref("1kg_eas_hg19")
print(gl.get_path("1kg_eas_hg19"))
gwaslab download ref 1kg_eas_hg19
gwaslab path 1kg_eas_hg19
Direct Hub URL (basename is the local filename download_ref writes):
https://huggingface.co/datasets/Cloufield/gwaslab-reference/resolve/main/1kg/hg19/EAS.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz
Layout
| Path | GWASLab keyword(s) | Use |
|---|---|---|
1kg/hg19/*.vcf.gz (+ .tbi) |
1kg_{afr,amr,eas,eur,pan,sas}_hg19 |
LD / strand / AF (1KGP3v5, hg19) |
1kg/hg38/*.vcf.gz (+ .tbi) |
1kg_{afr,amr,eas,eur,pan,sas}_hg38 |
LD / strand / AF (1KG 30x, hg38) |
rsid/1kg_dbsnp151_*_auto.txt.gz |
1kg_dbsnp151_hg19_auto, 1kg_dbsnp151_hg38_auto |
SNPID–rsID tables (autosomes) |
eaf/PAN.hapmap3.*.EAF.tsv.gz |
1kg_hm3_hg19_eaf, 1kg_hm3_hg38_eaf |
HapMap3 EAF for ancestry |
recombination/recombination_hg*.tar.gz |
recombination_hg19, recombination_hg38 |
Regional recombination tracks |
examples/t2d_bbj.txt.gz |
(not a catalog keyword) | Tutorial BBJ T2D sumstats |
Ancestries: AFR, AMR, EAS, EUR, SAS, PAN (all 1KG super-populations combined). Multi-allelic variants were decomposed and normalized; INFO includes population AF.
Processing
1KG VCFs were processed by GWASLab for regional LD plots and strand inference. They are not a substitute for the official 1000 Genomes release files.
Citations
- GWASLab: He Y, Koido M, Shimmori Y, Kamatani Y. GWASLab: a Python package for processing and visualizing GWAS summary statistics. Jxiv (2023). https://doi.org/10.51094/jxiv.305
- 1000 Genomes Project: The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature (2015). 30x high-coverage data: Byrska-Bishop et al., Cell (2022).
- HapMap recombination maps: International HapMap Consortium.
- BBJ T2D example: Suzuki K et al. Identification of 28 new susceptibility loci for type 2 diabetes in the Japanese population. Nat Genet (2019). Source: http://jenger.riken.jp/
Redistribute and cite the original consortia terms for 1KG, HapMap, dbSNP-derived tables, and BBJ summary statistics.
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