Variant report

Variant	rs6697764
Chromosome Location	chr1:94738846-94738847
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 39 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10158261	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782980	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10874849	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11165101	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11165108	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165110	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165122	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11165132	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1120667	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11580251	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11585556	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12089927	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12741519	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12750249	0.99[ASN][1000 genomes]
rs12756032	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1620975	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1628833	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1687924	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1687927	0.89[AMR][1000 genomes]
rs1687935	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1687941	0.84[AMR][1000 genomes]
rs1687951	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1687954	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1687970	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1756245	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1756248	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1765618	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1765621	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1765626	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1765628	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1765632	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1765649	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1765650	0.82[AMR][1000 genomes]
rs2065971	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2065972	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2077424	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2172133	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2210161	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2786906	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3789687	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3814020	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6541340	0.83[CEU][hapmap];0.85[GIH][hapmap]
rs67070250	0.96[ASN][1000 genomes]
rs7540185	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs902338	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428510	chr1:94709575-94866655	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:39)

SNP	Gene	Cis/trans	Tissue	Source
rs6697764	XM_212377	trans	multi-tissue	Pritchard
rs6697764	HSS00014319	trans	multi-tissue	Pritchard
rs6697764	NFATC4	cis	Liver	GTEx
rs6697764	TMEM56	cis	multi-tissue	Pritchard
rs6697764	IL17RC	cis	Liver	GTEx
rs6697764	EXTL3	trans	multi-tissue	Pritchard
rs6697764	hCT1643865.3	trans	multi-tissue	Pritchard
rs6697764	LOC643219	cis	Liver	GTEx
rs6697764	H1FOO	cis	Liver	GTEx
rs6697764	SPANXE	trans	multi-tissue	Pritchard
rs6697764	hCT2287596	trans	multi-tissue	Pritchard
rs6697764	ARHGAP29	cis	Liver	GTEx
rs6697764	TBC1D4	trans	multi-tissue	Pritchard
rs6697764	PAX1	cis	Liver	GTEx
rs6697764	Contig35607_RC	cis	multi-tissue	Pritchard
rs6697764	MYL10	cis	Liver	GTEx
rs6697764	DR1	cis	multi-tissue	Pritchard
rs6697764	HSS00060946	trans	multi-tissue	Pritchard
rs6697764	FGF19	trans	multi-tissue	Pritchard
rs6697764	FGF19	cis	Liver	GTEx
rs6697764	ZNF445	trans	multi-tissue	Pritchard
rs6697764	PAX1	trans	multi-tissue	Pritchard
rs6697764	NM_138403	trans	multi-tissue	Pritchard
rs6697764	NDST1	trans	multi-tissue	Pritchard
rs6697764	H1FOO	trans	multi-tissue	Pritchard
rs6697764	TBC1D4	cis	Liver	GTEx
rs6697764	BC039544	trans	multi-tissue	Pritchard
rs6697764	ZNF445	cis	Liver	GTEx
rs6697764	BU539002	trans	multi-tissue	Pritchard
rs6697764	IL17RC	trans	multi-tissue	Pritchard
rs6697764	AF056455	trans	multi-tissue	Pritchard
rs6697764	SPANXD	cis	Liver	GTEx
rs6697764	NDST1	cis	Liver	GTEx
rs6697764	EXTL3	cis	Liver	GTEx
rs6697764	HSS00014308	trans	multi-tissue	Pritchard
rs6697764	HSS00178733	trans	multi-tissue	Pritchard
rs6697764	ARHGAP29	cis	multi-tissue	Pritchard
rs6697764	NFATC4	trans	multi-tissue	Pritchard
rs6697764	CDH13	cis	Liver	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94725800-94742600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:94730800-94743600	Weak transcription	Lung	lung
3	chr1:94731600-94740200	Weak transcription	Adipose Nuclei	Adipose
4	chr1:94734200-94748600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:94735600-94739200	Enhancers	NH-A	brain
6	chr1:94735600-94739200	Enhancers	NHDF-Ad	bronchial
7	chr1:94735800-94739000	Enhancers	HSMM	muscle
8	chr1:94736400-94742400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:94736800-94739600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr1:94736800-94740600	Enhancers	Osteobl	bone
11	chr1:94736800-94742400	Weak transcription	HSMMtube	muscle
12	chr1:94736800-94744800	Weak transcription	HUVEC	blood vessel
13	chr1:94737200-94742000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:94737600-94740200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:94738200-94739800	Enhancers	Stomach Mucosa	stomach
16	chr1:94738400-94742800	Weak transcription	NHLF	lung
17	chr1:94738400-94744600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:94738400-94750000	Weak transcription	Pancreas	Pancrea
19	chr1:94738400-94750000	Weak transcription	HMEC	breast
20	chr1:94738600-94739400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:94738600-94744400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:94738600-94750200	Weak transcription	Fetal Kidney	kidney
23	chr1:94738800-94739000	Enhancers	A549	lung
24	chr1:94738800-94739600	Weak transcription	Ovary	ovary
25	chr1:94738800-94742400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:94738800-94750600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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