Variant report

Variant	rs3852454
Chromosome Location	chr10:19750431-19750432
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 119 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10159624	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10159852	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10734018	0.98[EUR][1000 genomes]
rs10740902	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10740903	0.98[EUR][1000 genomes]
rs10740904	0.96[EUR][1000 genomes]
rs10740905	0.98[EUR][1000 genomes]
rs10740906	0.98[EUR][1000 genomes]
rs10740907	0.98[EUR][1000 genomes]
rs10740908	0.96[EUR][1000 genomes]
rs10764018	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10764020	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10764021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10764024	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10764026	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10764027	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10764028	0.98[EUR][1000 genomes]
rs10764029	0.97[EUR][1000 genomes]
rs10764030	0.97[EUR][1000 genomes]
rs10764036	0.98[EUR][1000 genomes]
rs10764038	0.98[EUR][1000 genomes]
rs10827480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10827481	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10827485	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs10827486	0.98[EUR][1000 genomes]
rs11010096	0.98[EUR][1000 genomes]
rs11010097	0.98[EUR][1000 genomes]
rs1332931	0.98[EUR][1000 genomes]
rs1332932	0.98[EUR][1000 genomes]
rs1332933	0.98[EUR][1000 genomes]
rs1338603	0.98[EUR][1000 genomes]
rs1819478	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1930507	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1930508	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2358398	0.90[EUR][1000 genomes]
rs2358399	0.98[EUR][1000 genomes]
rs2358400	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2358402	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2358403	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2358406	0.98[EUR][1000 genomes]
rs2884446	0.98[EUR][1000 genomes]
rs3844351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3852453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3852455	0.98[EUR][1000 genomes]
rs3852456	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3852457	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3852458	0.98[EUR][1000 genomes]
rs3852459	0.98[EUR][1000 genomes]
rs3904886	0.82[AFR][1000 genomes]
rs3904887	0.98[EUR][1000 genomes]
rs3904900	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3904901	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3904902	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4325199	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4451600	0.98[EUR][1000 genomes]
rs4598552	0.98[EUR][1000 genomes]
rs4747374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4748581	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4748582	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4748583	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4748584	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4748586	0.98[EUR][1000 genomes]
rs4748587	0.98[EUR][1000 genomes]
rs4748588	0.98[EUR][1000 genomes]
rs4748589	0.98[EUR][1000 genomes]
rs61843295	0.98[EUR][1000 genomes]
rs6481930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6481936	0.98[EUR][1000 genomes]
rs6481938	0.98[EUR][1000 genomes]
rs6481939	0.98[EUR][1000 genomes]
rs6481940	0.98[EUR][1000 genomes]
rs6481942	0.98[EUR][1000 genomes]
rs7073581	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7073687	0.98[EUR][1000 genomes]
rs7074596	0.98[EUR][1000 genomes]
rs7077318	0.98[EUR][1000 genomes]
rs7077661	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7081165	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7088993	0.98[EUR][1000 genomes]
rs7090766	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7090914	0.96[EUR][1000 genomes]
rs7093985	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7095412	0.98[EUR][1000 genomes]
rs7099401	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7902270	0.98[EUR][1000 genomes]
rs7902768	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7903569	0.98[EUR][1000 genomes]
rs7904642	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7906538	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7913355	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7917509	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7918304	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7919278	0.98[EUR][1000 genomes]
rs7919478	0.98[EUR][1000 genomes]
rs7922824	0.98[EUR][1000 genomes]
rs7922998	0.98[EUR][1000 genomes]
rs997845	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv466764	chr10:19400845-19979434	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv550128	chr10:19400845-19979434	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2750885	chr10:19407891-19836364	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1043780	chr10:19415575-19827284	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1035870	chr10:19415575-19832047	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv550129	chr10:19417181-19834795	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1035591	chr10:19417883-19823164	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv540506	chr10:19417883-19823164	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv2750886	chr10:19432774-19832094	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1047513	chr10:19461947-19810770	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv540507	chr10:19461947-19810770	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv894919	chr10:19514636-19758398	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	esv2759737	chr10:19694144-20024994	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv894930	chr10:19696007-19793195	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	esv2758211	chr10:19714637-20024994	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
16	nsv466766	chr10:19726945-19758593	Weak transcription Enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv550135	chr10:19726945-19758593	Enhancers Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv1049295	chr10:19740296-20509036	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
19	nsv8605	chr10:19746007-19754802	Strong transcription Weak transcription	n/a	n/a	inside rSNPs	diseases
20	nsv1042877	chr10:19749314-20067572	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
21	esv1851047	chr10:19749522-19752137	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases
22	esv10793	chr10:19749801-19758983	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:19740000-19781200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr10:19750200-19751400	Strong transcription	Fetal Intestine Large	intestine
3	chr10:19750400-19750800	Strong transcription	Fetal Intestine Small	intestine

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