Variant report

Variant	rs10862992
Chromosome Location	chr12:85925154-85925155
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10083104	0.82[ASN][1000 genomes]
rs10466964	0.81[ASN][1000 genomes]
rs10779163	0.90[EUR][1000 genomes]
rs10779165	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10779166	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10779174	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10779179	0.89[ASN][1000 genomes]
rs10862989	1.00[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10862994	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10862995	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10862997	0.81[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs10862998	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10863006	0.88[ASN][1000 genomes]
rs10863019	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10863021	0.89[ASN][1000 genomes]
rs10863022	0.86[ASN][1000 genomes]
rs10863023	0.86[ASN][1000 genomes]
rs10863031	0.82[ASN][1000 genomes]
rs10863034	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs10863035	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs11116813	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11116838	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11116850	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11116851	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11116853	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11116857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116913	0.90[ASN][1000 genomes]
rs11116933	0.88[ASN][1000 genomes]
rs12230791	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12303708	0.90[ASN][1000 genomes]
rs12311475	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12318024	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1547544	0.81[EUR][1000 genomes]
rs17013043	0.83[ASN][1000 genomes]
rs1870936	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2199510	0.83[ASN][1000 genomes]
rs2199515	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28637596	0.83[ASN][1000 genomes]
rs2897092	0.81[ASN][1000 genomes]
rs4143506	0.90[ASN][1000 genomes]
rs4761064	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4761080	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6539898	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67352195	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7308482	0.86[ASN][1000 genomes]
rs7310496	0.83[ASN][1000 genomes]
rs7397867	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7485843	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7488757	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7488922	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7975674	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7976228	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:85921400-85925200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:85921600-85926200	Enhancers	Fetal Intestine Small	intestine
3	chr12:85923200-85926200	Enhancers	Fetal Intestine Large	intestine
4	chr12:85925000-85925400	Active TSS	GM12878-XiMat	blood

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