Variant report

Variant	rs11161663
Chromosome Location	chr1:86185323-86185324
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1047892	0.85[CEU][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1047893	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1047895	0.93[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10873716	0.93[CEU][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10873717	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161643	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs11161645	0.86[JPT][hapmap]
rs11161649	0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs11161650	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11161651	0.93[CEU][hapmap];0.80[JPT][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11161654	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161656	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11161657	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161658	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161659	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11161660	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11161661	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161662	0.91[ASN][1000 genomes]
rs11161664	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11161665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161667	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11578464	0.85[CEU][hapmap]
rs12058974	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12063702	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12089500	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12097932	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12128916	0.90[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs12564080	0.88[ASN][1000 genomes]
rs12566746	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12739713	0.86[ASN][1000 genomes]
rs12752817	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12756013	0.87[ASN][1000 genomes]
rs12757270	0.85[ASN][1000 genomes]
rs12758511	0.87[ASN][1000 genomes]
rs1539444	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1764285	0.93[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1764288	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1764289	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1764291	0.90[CEU][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1764292	0.90[CEU][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1764299	0.90[CEU][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1775988	0.93[CEU][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1775990	0.84[CEU][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1889919	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1889920	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2389970	0.86[JPT][hapmap]
rs2389972	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2785081	0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs2995537	0.90[CEU][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs373787	0.90[CEU][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes]
rs3753786	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3753789	0.92[CEU][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3753790	0.93[CEU][hapmap];0.80[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3767162	0.84[EUR][1000 genomes]
rs414618	0.86[JPT][hapmap]
rs418979	0.90[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs419409	0.87[EUR][1000 genomes]
rs424205	0.86[EUR][1000 genomes]
rs434853	0.87[EUR][1000 genomes]
rs447446	0.87[EUR][1000 genomes]
rs4912441	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61783617	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6576784	0.86[ASN][1000 genomes]
rs6667094	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6672312	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6689168	0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6697535	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699497	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7518312	0.82[ASN][1000 genomes]
rs7520491	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs7532758	0.93[CEU][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs7554844	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs821379	0.84[EUR][1000 genomes]
rs821381	0.84[EUR][1000 genomes]
rs821386	0.93[CEU][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs821389	0.93[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs821393	0.83[JPT][hapmap]
rs821401	0.84[EUR][1000 genomes]
rs9324154	0.82[EUR][1000 genomes]
rs952837	0.90[CEU][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9700177	0.85[EUR][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11161663	C1orf181	cis	multi-tissue	Pritchard
rs11161663	ZNHIT6	cis	Adipose Subcutaneous	GTEx
rs11161663	C1orf181	Cis_1M	lymphoblastoid	RTeQTL
rs11161663	ZNHIT6	cis	Artery Aorta	GTEx
rs11161663	ZNHIT6	cis	Esophagus Muscularis	GTEx
rs11161663	ZNHIT6	cis	lung	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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