Variant report

Variant	rs3965496
Chromosome Location	chr19:24389074-24389075
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10407459	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10412660	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10426547	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10500224	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1830165	0.91[AFR][1000 genomes]
rs1830167	0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1852404	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1852408	0.82[ASN][1000 genomes]
rs1896751	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1918156	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1975188	0.82[AMR][1000 genomes]
rs2082492	0.80[AMR][1000 genomes]
rs2160743	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2278443	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2335150	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2463047	0.91[AFR][1000 genomes]
rs2840002	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28750988	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28759392	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28829917	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28840169	0.94[ASN][1000 genomes]
rs4045848	0.91[AFR][1000 genomes]
rs4332857	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4507031	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4556916	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4637035	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4932745	0.80[AMR][1000 genomes]
rs4986238	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4986276	0.88[ASN][1000 genomes]
rs56157198	0.94[ASN][1000 genomes]
rs7252482	0.80[AMR][1000 genomes]
rs7339516	0.88[ASN][1000 genomes]
rs7508396	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8100720	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8101475	0.88[ASN][1000 genomes]
rs8189902	0.87[AFR][1000 genomes]
rs8189903	0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs8189914	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9916992	0.82[ASN][1000 genomes]
rs9917098	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:58 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063538	chr19:23671507-24561180	Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1065058	chr19:23724151-24503722	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv524183	chr19:23742358-24490299	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv1063173	chr19:23821984-24521623	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1056903	chr19:23827708-24503722	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv1066151	chr19:23830504-24561180	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv911472	chr19:23896204-24601680	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv911473	chr19:23901285-24545366	Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv1061681	chr19:23912494-24507160	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv1058987	chr19:23913386-24503722	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv543968	chr19:23913386-24503722	Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv911475	chr19:23957937-24545366	Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
13	nsv579077	chr19:24084419-24490299	Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
14	nsv579078	chr19:24209547-24631604	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
15	nsv911477	chr19:24217064-24545366	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
16	nsv432043	chr19:24222128-24503985	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
17	nsv911478	chr19:24241624-24545366	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
18	nsv833793	chr19:24269209-24424795	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
19	nsv911479	chr19:24284455-24482072	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
20	nsv911481	chr19:24300810-24471107	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
21	nsv911482	chr19:24300810-24482072	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
22	esv34504	chr19:24339720-24503985	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
23	esv2757692	chr19:24339720-24505637	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
24	esv2758751	chr19:24339720-24557363	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
25	nsv1058057	chr19:24346067-24596738	ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
26	nsv1059342	chr19:24348669-24596738	ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	esv2758492	chr19:24350565-24557363	ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
28	nsv1066250	chr19:24352103-24596738	ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
29	nsv458531	chr19:24354312-24490299	Active TSS ZNF genes & repeats Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
30	nsv579080	chr19:24354312-24490299	ZNF genes & repeats Weak transcription Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
31	nsv1058203	chr19:24354312-24596738	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
32	nsv1057364	chr19:24356132-24444086	ZNF genes & repeats Weak transcription Enhancers Active TSS	n/a	n/a	inside rSNPs	diseases
33	nsv543971	chr19:24356132-24444086	Weak transcription ZNF genes & repeats Enhancers Active TSS	n/a	n/a	inside rSNPs	diseases
34	nsv1060568	chr19:24356132-24487889	ZNF genes & repeats Active TSS Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
35	nsv1065409	chr19:24356132-24503722	ZNF genes & repeats Active TSS Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
36	nsv1063458	chr19:24357581-24596738	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
37	nsv510760	chr19:24366161-24437000	ZNF genes & repeats Weak transcription Active TSS Enhancers	n/a	n/a	inside rSNPs	diseases
38	nsv1055574	chr19:24367758-24464945	ZNF genes & repeats Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
39	nsv1055774	chr19:24367758-24596738	Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
40	nsv1055655	chr19:24373083-24462409	ZNF genes & repeats Active TSS Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
41	nsv458532	chr19:24374419-24490299	ZNF genes & repeats Weak transcription Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
42	nsv579081	chr19:24374419-24490299	ZNF genes & repeats Active TSS Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
43	nsv1060443	chr19:24375437-24464945	ZNF genes & repeats Weak transcription Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
44	esv2763110	chr19:24375449-24487682	ZNF genes & repeats Active TSS Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
45	nsv517869	chr19:24378197-24490299	ZNF genes & repeats Active TSS Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
46	nsv911483	chr19:24378400-24545366	ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
47	nsv1056981	chr19:24379090-24464945	ZNF genes & repeats Active TSS Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
48	nsv1062273	chr19:24379090-24487682	ZNF genes & repeats Active TSS Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
49	nsv1064250	chr19:24379090-24503773	ZNF genes & repeats Weak transcription Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
50	nsv1066978	chr19:24379090-24504093	ZNF genes & repeats Active TSS Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3965496	CTD-2017D11.1	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:24385400-24389600	ZNF genes & repeats	Liver	Liver
2	chr19:24387200-24389400	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:24387400-24389600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum

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