Variant report

Variant	rs10782967
Chromosome Location	chr1:94211974-94211975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94210546..94213196-chr1:94216011..94218265,2	K562	blood:
2	chr1:94210546..94212341-chr1:94215230..94217511,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10489602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10489603	0.91[GIH][hapmap]
rs10489604	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs10782966	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11165020	0.89[EUR][1000 genomes]
rs11165022	0.83[JPT][hapmap]
rs11165024	0.87[EUR][1000 genomes]
rs11165026	0.83[JPT][hapmap]
rs12027630	0.85[EUR][1000 genomes]
rs12041975	0.83[JPT][hapmap]
rs12122113	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12123957	0.83[EUR][1000 genomes]
rs12134359	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12137687	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12140446	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs12143274	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12143279	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12563731	0.87[EUR][1000 genomes]
rs12565614	0.88[EUR][1000 genomes]
rs12565817	0.91[GIH][hapmap]
rs12566531	0.87[EUR][1000 genomes]
rs12734571	0.85[EUR][1000 genomes]
rs12739186	0.89[EUR][1000 genomes]
rs12745990	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1398798	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1884018	0.96[CEU][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs1980083	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs2143990	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2143992	0.83[JPT][hapmap]
rs2235971	0.86[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs2391315	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs2391322	0.92[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs2747039	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2747041	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2747043	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2747045	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2747050	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2818160	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2818162	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2818164	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2818169	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3000471	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3747965	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs4075523	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4141736	0.85[EUR][1000 genomes]
rs4141737	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs4240955	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4240956	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4314890	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4350209	0.86[ASW][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4847253	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4847255	0.81[EUR][1000 genomes]
rs4847256	0.85[CEU][hapmap]
rs4847264	0.83[JPT][hapmap]
rs6663218	0.82[JPT][hapmap]
rs6664719	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs6681265	0.82[JPT][hapmap]
rs6685747	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7364910	0.88[EUR][1000 genomes]
rs743111	0.82[JPT][hapmap]
rs8179391	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs871854	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10782967	RP11-488P3.1	cis	Stomach	GTEx
rs10782967	RP11-488P3.1	cis	lung	GTEx
rs10782967	RP11-488P3.1	cis	Artery Tibial	GTEx
rs10782967	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs10782967	RP11-488P3.1	cis	Nerve Tibial	GTEx
rs10782967	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs10782967	RP11-488P3.1	cis	Thyroid	GTEx
rs10782967	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs10782967	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx
rs10782967	RP11-488P3.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94199400-94217400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:94206000-94212600	Weak transcription	HMEC	breast
3	chr1:94206800-94212400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:94206800-94212400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:94208200-94215600	Weak transcription	Aorta	Aorta
6	chr1:94209400-94212400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:94209400-94212600	Enhancers	NHEK	skin
8	chr1:94209800-94212600	Enhancers	Fetal Thymus	thymus
9	chr1:94210200-94212600	Enhancers	Esophagus	oesophagus
10	chr1:94210800-94215600	Weak transcription	Thymus	Thymus
11	chr1:94211000-94212400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:94211600-94212000	Enhancers	Hela-S3	cervix
13	chr1:94211800-94212400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:94211800-94215600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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