Variant report

Variant	rs17684859
Chromosome Location	chr3:158213841-158213842
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10936131	0.83[TSI][hapmap]
rs10936143	0.86[CEU][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10936144	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10936145	0.91[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11707386	0.83[TSI][hapmap]
rs11708784	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11710813	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11716327	0.83[TSI][hapmap]
rs12491598	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12492884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12494926	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12495085	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12496934	0.83[TSI][hapmap]
rs12631704	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1656368	0.97[ASN][1000 genomes]
rs1656369	0.97[ASN][1000 genomes]
rs16829104	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16829122	0.82[YRI][hapmap]
rs17628958	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17628988	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17683939	0.80[MEX][hapmap]
rs28431969	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4402974	0.83[TSI][hapmap]
rs4680435	0.83[TSI][hapmap]
rs4680441	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55720154	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55765541	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55842512	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6784511	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6784968	0.83[TSI][hapmap]
rs6788907	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6806967	0.82[CEU][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73154304	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73154306	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73154307	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154309	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73154313	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73154314	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73154326	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73154329	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73154331	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73154340	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73172114	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73172119	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73172134	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7613528	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7649643	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1014381	chr3:158070451-158350118	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1013046	chr3:158176582-158244606	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1014557	chr3:158176582-158251602	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv877690	chr3:158184263-158296916	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs17684859	RSRC1	Cis_1M	lymphoblastoid	RTeQTL
rs17684859	LXN	cis	lymphoblastoid	seeQTL
rs17684859	RP11-538P18.2	cis	lung	GTEx
rs17684859	RP11-538P18.2	cis	Skin Sun Exposed Lower leg	GTEx
rs17684859	RSRC1	cis	normal skin	skin_eQTL
rs17684859	RSRC1	cis	Adipose Subcutaneous	GTEx
rs17684859	RP11-538P18.2	cis	Nerve Tibial	GTEx
rs17684859	RSRC1	cis	cerebellum	SCAN
rs17684859	TIPARP	cis	parietal	SCAN
rs17684859	RP11-538P18.2	cis	Artery Tibial	GTEx
rs17684859	SSR3	cis	cerebellum	SCAN
rs17684859	SHOX2	cis	lymphoblastoid	seeQTL
rs17684859	RP11-538P18.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158207200-158221400	Weak transcription	Ovary	ovary
2	chr3:158211200-158215200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:158211600-158221400	Weak transcription	Gastric	stomach

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