Variant report

Variant	rs12231930
Chromosome Location	chr12:85949845-85949846
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:85949711..85951775-chr12:85954587..85956542,2	K562	blood:

Extended variants
information (count: 169 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs10863013	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863014	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863024	0.93[ASN][1000 genomes]
rs10863025	0.93[ASN][1000 genomes]
rs10863030	0.90[ASN][1000 genomes]
rs10863042	0.87[ASN][1000 genomes]
rs10863051	0.89[ASN][1000 genomes]
rs11116805	0.97[EUR][1000 genomes]
rs11116806	0.95[EUR][1000 genomes]
rs11116808	0.97[EUR][1000 genomes]
rs11116812	0.97[EUR][1000 genomes]
rs11116815	0.97[EUR][1000 genomes]
rs11116830	0.97[EUR][1000 genomes]
rs11116852	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11116861	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116866	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116867	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116868	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116869	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116870	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116873	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11116874	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116875	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116876	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116880	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116881	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116882	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116884	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116885	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116887	1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116889	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116890	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116892	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116895	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116896	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116898	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116899	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116920	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116932	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11116936	0.93[ASN][1000 genomes]
rs11116938	0.93[ASN][1000 genomes]
rs11116944	0.90[ASN][1000 genomes]
rs11116950	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11116970	0.89[ASN][1000 genomes]
rs11116973	0.89[ASN][1000 genomes]
rs11116977	0.89[ASN][1000 genomes]
rs11513953	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11832292	0.87[ASN][1000 genomes]
rs11833053	0.89[ASN][1000 genomes]
rs11835255	0.87[ASN][1000 genomes]
rs12227817	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12228112	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12228412	0.89[ASN][1000 genomes]
rs12228703	0.87[ASN][1000 genomes]
rs12230759	0.97[EUR][1000 genomes]
rs12230925	0.97[EUR][1000 genomes]
rs12231153	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12231156	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12231815	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12308539	0.87[ASN][1000 genomes]
rs12308540	0.87[ASN][1000 genomes]
rs12308608	0.87[ASN][1000 genomes]
rs12316799	0.87[ASN][1000 genomes]
rs12316860	0.87[ASN][1000 genomes]
rs1398443	0.97[EUR][1000 genomes]
rs1512728	0.97[EUR][1000 genomes]
rs1512729	0.97[EUR][1000 genomes]
rs1564123	0.89[ASN][1000 genomes]
rs17013154	0.87[ASN][1000 genomes]
rs2203199	0.97[EUR][1000 genomes]
rs2405253	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34506479	0.87[ASN][1000 genomes]
rs3884595	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143507	0.89[ASN][1000 genomes]
rs4409917	0.92[ASN][1000 genomes]
rs4554972	0.90[ASN][1000 genomes]
rs55827526	0.87[ASN][1000 genomes]
rs55897040	0.97[EUR][1000 genomes]
rs55897445	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56251198	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57059247	0.97[EUR][1000 genomes]
rs57527697	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57608040	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57741929	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58809157	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59312748	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59403304	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59712244	0.97[EUR][1000 genomes]
rs59788521	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59846618	1.00[EUR][1000 genomes]
rs60202749	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60552633	0.97[EUR][1000 genomes]
rs60683378	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539908	0.87[ASN][1000 genomes]
rs6539909	0.87[ASN][1000 genomes]
rs7131964	0.89[ASN][1000 genomes]
rs7137284	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297228	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7300664	0.97[EUR][1000 genomes]
rs7304792	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308668	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7313388	0.87[ASN][1000 genomes]
rs73367235	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367237	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367241	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367246	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367251	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367261	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367266	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367273	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73368476	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73368490	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73368493	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73370465	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74112007	0.97[EUR][1000 genomes]
rs74112008	0.97[EUR][1000 genomes]
rs74112009	0.97[EUR][1000 genomes]
rs74112028	0.97[EUR][1000 genomes]
rs74112030	0.97[EUR][1000 genomes]
rs74112031	0.97[EUR][1000 genomes]
rs74112083	0.97[EUR][1000 genomes]
rs74112086	0.95[EUR][1000 genomes]
rs74112222	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74112251	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74112259	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74112289	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74112507	0.89[ASN][1000 genomes]
rs7484736	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7485150	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7485219	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7486870	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7486887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7486989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7489034	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952944	0.97[EUR][1000 genomes]
rs7958126	0.97[EUR][1000 genomes]
rs7961629	0.97[EUR][1000 genomes]
rs7963815	0.86[EUR][1000 genomes]
rs7966534	0.92[EUR][1000 genomes]
rs7972133	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976869	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7977072	0.94[ASN][1000 genomes]
rs922340	0.87[ASN][1000 genomes]
rs9783419	0.97[EUR][1000 genomes]
rs9783509	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9783510	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9783520	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9943733	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943736	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9943770	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943779	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9989016	0.85[ASN][1000 genomes]
rs9989038	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv1043663	chr12:85934317-85999874	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv523422	chr12:85939419-85995733	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv1050959	chr12:85941487-85999874	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12231930	LOC254559	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:85945400-85952200	Weak transcription	Duodenum Mucosa	Duodenum

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