Variant report

Variant	rs2645994
Chromosome Location	chr9:115483322-115483323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 156 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10115576	0.82[TSI][hapmap]
rs10115711	1.00[ASN][1000 genomes]
rs10124260	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs10124979	1.00[ASN][1000 genomes]
rs10733594	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs10733598	1.00[ASN][1000 genomes]
rs10733599	1.00[ASN][1000 genomes]
rs10739370	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs10739373	0.85[CEU][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs10739374	1.00[ASN][1000 genomes]
rs10739376	1.00[ASN][1000 genomes]
rs10759590	1.00[ASN][1000 genomes]
rs10759603	1.00[ASN][1000 genomes]
rs10759604	1.00[ASN][1000 genomes]
rs1158331	1.00[ASN][1000 genomes]
rs11791531	1.00[ASN][1000 genomes]
rs1324931	0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs1361720	0.85[CEU][hapmap]
rs1418409	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs1418410	1.00[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs1475293	0.82[TSI][hapmap]
rs1539338	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs1570754	1.00[ASN][1000 genomes]
rs1693411	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1711739	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1711744	0.85[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs1711745	1.00[CEU][hapmap]
rs1711746	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1711747	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1832890	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1891402	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs1891403	0.85[CEU][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs1965335	0.90[EUR][1000 genomes]
rs2025544	0.87[GIH][hapmap];1.00[ASN][1000 genomes]
rs2051018	1.00[ASN][1000 genomes]
rs2147643	1.00[ASN][1000 genomes]
rs2147646	1.00[ASN][1000 genomes]
rs2153837	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182048	1.00[ASN][1000 genomes]
rs2185768	0.87[GIH][hapmap];0.84[TSI][hapmap]
rs2185769	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645985	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645991	0.86[EUR][1000 genomes]
rs2645993	0.85[CEU][hapmap]
rs2796025	1.00[ASN][1000 genomes]
rs2796028	0.85[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796031	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796035	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796037	0.81[EUR][1000 genomes]
rs2798316	0.87[GIH][hapmap];0.84[TSI][hapmap]
rs2995805	0.81[EUR][1000 genomes]
rs4246892	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs4304397	0.85[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs4360356	1.00[ASN][1000 genomes]
rs4549852	1.00[ASN][1000 genomes]
rs4978507	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs4978510	1.00[ASN][1000 genomes]
rs4979153	0.85[CEU][hapmap]
rs4979154	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs4979155	1.00[ASN][1000 genomes]
rs4979157	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs4979165	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs4979183	1.00[ASN][1000 genomes]
rs4979184	1.00[ASN][1000 genomes]
rs4979186	1.00[ASN][1000 genomes]
rs55912580	1.00[ASN][1000 genomes]
rs6477959	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs700122	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs7026450	1.00[ASN][1000 genomes]
rs7030795	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs7038684	1.00[ASN][1000 genomes]
rs7040954	1.00[ASN][1000 genomes]
rs7041965	1.00[ASN][1000 genomes]
rs7047914	1.00[ASN][1000 genomes]
rs72768411	0.90[EUR][1000 genomes]
rs7859175	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs7862183	0.82[EUR][1000 genomes]
rs7868830	0.85[CEU][hapmap]
rs7869100	1.00[ASN][1000 genomes]
rs786961	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786965	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786966	0.85[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786967	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786968	1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786969	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786972	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786973	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786974	0.86[EUR][1000 genomes]
rs786977	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786978	0.85[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs786979	0.81[EUR][1000 genomes]
rs786981	0.83[EUR][1000 genomes]
rs786983	0.83[EUR][1000 genomes]
rs7872628	1.00[ASN][1000 genomes]
rs787271	0.85[CEU][hapmap];0.88[TSI][hapmap]
rs787272	0.82[CEU][hapmap]
rs787275	0.82[CEU][hapmap]
rs787276	0.85[CEU][hapmap]
rs787278	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787280	0.85[CEU][hapmap];0.88[TSI][hapmap]
rs787281	1.00[ASN][1000 genomes]
rs787284	0.85[CEU][hapmap]
rs787285	1.00[ASN][1000 genomes]
rs787286	1.00[ASN][1000 genomes]
rs787287	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs787291	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787292	0.88[EUR][1000 genomes]
rs787294	0.85[CEU][hapmap]
rs787295	0.85[CEU][hapmap];0.88[TSI][hapmap]
rs787296	1.00[ASN][1000 genomes]
rs787297	0.85[CEU][hapmap];0.88[TSI][hapmap]
rs787298	0.85[CEU][hapmap]
rs787299	0.85[CEU][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs787301	0.85[CEU][hapmap];0.88[TSI][hapmap]
rs787302	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs787303	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7873289	1.00[ASN][1000 genomes]
rs813101	0.85[CEU][hapmap]
rs885387	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs912662	1.00[ASN][1000 genomes]
rs9409123	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs947609	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs980345	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv515899	chr9:115359049-115593870	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv34346	chr9:115360505-115581453	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1038999	chr9:115367078-115590950	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats 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	15 gene(s)	inside rSNPs	diseases
6	esv2757350	chr9:115371397-115594108	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv471317	chr9:115375153-115558246	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	esv2761275	chr9:115376461-115590962	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1035169	chr9:115378282-115573581	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1049451	chr9:115378282-115585109	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1047374	chr9:115378282-115590950	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1038306	chr9:115379305-115595695	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv540194	chr9:115379305-115595695	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv1051909	chr9:115379505-115588377	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv540195	chr9:115379505-115588377	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv915763	chr9:115379600-115588349	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	esv3693040	chr9:115381164-115578065	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	nsv515121	chr9:115383227-115585827	Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
19	nsv1044168	chr9:115383253-115585109	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
20	nsv1048327	chr9:115383253-115589646	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
21	nsv1044381	chr9:115383253-115590950	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
22	nsv442163	chr9:115383255-115590578	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
23	esv35051	chr9:115383332-115573581	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
24	esv34763	chr9:115383332-115581453	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
25	nsv430090	chr9:115383445-115594445	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
26	nsv1041424	chr9:115389428-115590950	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
27	nsv1050186	chr9:115390759-115550453	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
28	nsv1047625	chr9:115390759-115587347	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
29	nsv540196	chr9:115390759-115587347	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
30	nsv615198	chr9:115397206-115589251	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
31	nsv893733	chr9:115397206-115712068	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
32	nsv1051808	chr9:115397891-115590950	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
33	esv34739	chr9:115409445-115581453	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2645994	TSCOT	cis	multi-tissue	Pritchard

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115480800-115493400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:115481000-115488000	Weak transcription	HepG2	liver
3	chr9:115481200-115488000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr9:115482200-115483400	Enhancers	Fetal Intestine Small	intestine
5	chr9:115482200-115488200	Weak transcription	Adipose Nuclei	Adipose
6	chr9:115482400-115483600	Enhancers	Fetal Intestine Large	intestine

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