Variant report

Variant	rs12097932
Chromosome Location	chr1:86182216-86182217
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs1047893	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1047895	0.85[CEU][hapmap]
rs10873716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873717	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11161649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11161650	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161654	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11161656	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161657	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11161658	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11161659	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11161660	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161661	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11161662	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11161663	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11161664	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161665	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11161667	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12058974	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12063702	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12067749	0.81[AFR][1000 genomes]
rs12075929	0.82[LWK][hapmap]
rs12089500	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12128916	0.85[CEU][hapmap]
rs12564080	0.92[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12566746	0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12738010	0.87[ASN][1000 genomes]
rs12739713	0.84[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12752817	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12756013	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12757270	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12758511	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1539444	0.85[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1764285	0.85[CEU][hapmap]
rs1764291	0.85[CEU][hapmap]
rs1764292	0.85[CEU][hapmap]
rs1764299	0.85[CEU][hapmap]
rs1775988	0.85[CEU][hapmap]
rs1775990	0.88[CEU][hapmap]
rs1889919	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1889920	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2069208	0.84[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[ASN][1000 genomes]
rs2389972	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2995537	0.85[CEU][hapmap]
rs35438778	0.83[ASN][1000 genomes]
rs373787	0.85[CEU][hapmap]
rs3753786	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3753789	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];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3753790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs418979	0.85[CEU][hapmap]
rs6576784	0.84[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6672312	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6689168	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6697535	0.92[CEU][hapmap];0.87[CHB][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7518312	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7520491	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs7532758	0.85[CEU][hapmap]
rs7554844	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs821386	0.89[CEU][hapmap]
rs821389	0.85[CEU][hapmap]
rs952837	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv871471	chr1:86143084-86211516	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12097932	C1orf181	cis	multi-tissue	Pritchard
rs12097932	C1orf52	cis	cerebellum	SCAN
rs12097932	ZNHIT6	cis	Adipose Subcutaneous	GTEx
rs12097932	ZNHIT6	cis	lung	GTEx
rs12097932	ZNHIT6	cis	Artery Aorta	GTEx
rs12097932	C1orf181	Cis_1M	lymphoblastoid	RTeQTL
rs12097932	ZNHIT6	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86174400-86185800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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