Variant report

Variant	rs10862993
Chromosome Location	chr12:85925338-85925339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10746344	0.84[EUR][1000 genomes]
rs10746346	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10746347	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10779161	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10779164	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10779167	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10779168	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10779169	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10779170	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10779173	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10779180	0.88[ASN][1000 genomes]
rs10779181	0.87[ASN][1000 genomes]
rs10779182	0.85[ASN][1000 genomes]
rs10779188	0.83[ASN][1000 genomes]
rs10862979	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10862989	0.82[GIH][hapmap]
rs10862990	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10862991	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10862999	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10863000	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10863007	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10863008	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10863032	0.85[ASN][1000 genomes]
rs11116807	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11116832	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11116833	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11116930	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11116934	0.88[ASN][1000 genomes]
rs11116935	0.88[ASN][1000 genomes]
rs11116965	0.82[ASN][1000 genomes]
rs11116966	0.83[ASN][1000 genomes]
rs11116967	0.83[ASN][1000 genomes]
rs11116968	0.83[ASN][1000 genomes]
rs11116969	0.83[ASN][1000 genomes]
rs11831266	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11835161	0.87[ASN][1000 genomes]
rs12578708	0.89[ASN][1000 genomes]
rs1398440	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1398442	0.91[ASN][1000 genomes]
rs1870933	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1870935	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2199508	0.86[ASN][1000 genomes]
rs2199511	0.87[ASN][1000 genomes]
rs2199512	0.87[ASN][1000 genomes]
rs2199513	0.89[ASN][1000 genomes]
rs2199516	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2199517	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2199518	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2219711	0.86[ASN][1000 genomes]
rs2405248	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2405254	0.89[ASN][1000 genomes]
rs2405256	0.87[ASN][1000 genomes]
rs2405257	0.85[ASN][1000 genomes]
rs4761063	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4897817	0.88[ASN][1000 genomes]
rs4897825	0.87[ASN][1000 genomes]
rs4897842	0.82[ASN][1000 genomes]
rs4897843	0.83[ASN][1000 genomes]
rs6419420	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6419421	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6539899	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6539901	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6539902	0.87[ASN][1000 genomes]
rs7133064	0.87[ASN][1000 genomes]
rs7133855	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7134486	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7136236	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7295445	0.87[ASN][1000 genomes]
rs7297262	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7300800	0.81[ASN][1000 genomes]
rs7302629	0.87[ASN][1000 genomes]
rs7303316	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7304475	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7316167	0.89[ASN][1000 genomes]
rs7485084	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7485590	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7486767	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7487599	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7955601	0.85[ASN][1000 genomes]
rs7957797	0.92[ASN][1000 genomes]
rs7966898	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7973153	0.85[ASN][1000 genomes]
rs7973323	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7977259	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs898986	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9788015	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9788074	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1792335	chr12:85321249-86003609	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv817242	chr12:85622245-86069213	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1054573	chr12:85658602-86235433	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1035600	chr12:85661373-86235433	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1053044	chr12:85843030-85942504	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1036617	chr12:85855093-86010549	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv2751125	chr12:85884858-86098240	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1043253	chr12:85888151-86125364	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv795	chr12:85893392-85938122	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1041556	chr12:85897131-85934317	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1037938	chr12:85902517-86045125	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	esv2761758	chr12:85906092-86045137	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv455679	chr12:85908396-86024749	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv559664	chr12:85908396-86024749	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv559665	chr12:85908396-86070692	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	esv2751126	chr12:85912432-86061403	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv520857	chr12:85919312-85927862	Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10862993	NTS	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:85921600-85926200	Enhancers	Fetal Intestine Small	intestine
2	chr12:85923200-85926200	Enhancers	Fetal Intestine Large	intestine
3	chr12:85925000-85925400	Active TSS	GM12878-XiMat	blood

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