Variant report

Variant	rs2498437
Chromosome Location	chr9:71791480-71791481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71790152..71792261-chr9:71797735..71799818,2	MCF-7	breast:
2	chr9:71789625..71792443-chr9:71836331..71838562,2	K562	blood:
3	chr9:71733168..71738729-chr9:71786929..71793777,10	MCF-7	breast:
4	chr9:71668853..71671288-chr9:71790657..71793201,2	MCF-7	breast:
5	chr9:71734142..71739001-chr9:71788032..71795507,11	MCF-7	breast:
6	chr9:71668771..71670774-chr9:71790512..71793503,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119139	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10156634	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10156651	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10735653	0.89[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10781434	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10781435	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11791970	1.00[ASN][1000 genomes]
rs12551317	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12551566	1.00[ASN][1000 genomes]
rs12553945	1.00[ASN][1000 genomes]
rs12555245	1.00[ASN][1000 genomes]
rs2993817	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2993822	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002381	0.89[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34774441	1.00[ASN][1000 genomes]
rs41277913	1.00[ASN][1000 genomes]
rs4567104	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4745625	0.89[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4745626	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4745627	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62567098	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62567099	1.00[ASN][1000 genomes]
rs6560586	0.90[EUR][1000 genomes]
rs7020849	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7030890	0.90[EUR][1000 genomes]
rs7875573	0.89[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9411187	0.89[CEU][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9411202	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9411203	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
6	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv1051798	chr9:71511805-71792032	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv466397	chr9:71574757-71843023	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv614550	chr9:71574757-71843023	Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
16	nsv1050692	chr9:71578494-71843023	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv893416	chr9:71597840-71888601	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
18	nsv1040539	chr9:71600042-71844108	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	nsv540149	chr9:71600042-71844108	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
20	nsv949664	chr9:71607398-71842391	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
21	nsv948708	chr9:71632265-71842391	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
22	nsv1037787	chr9:71635338-71807648	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
23	nsv540151	chr9:71635338-71807648	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
24	nsv817209	chr9:71675454-71829412	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
25	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
26	nsv508550	chr9:71679166-71809433	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
27	nsv893427	chr9:71762766-71858517	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71788200-71797200	Enhancers	Stomach Mucosa	stomach
2	chr9:71788800-71792000	Active TSS	Liver	Liver
3	chr9:71789400-71791600	Flanking Active TSS	HepG2	liver
4	chr9:71789400-71792400	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr9:71789600-71792000	Weak transcription	Gastric	stomach
6	chr9:71789800-71792400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:71790000-71791800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr9:71790000-71792000	Enhancers	Hela-S3	cervix
9	chr9:71790200-71791600	Enhancers	Duodenum Mucosa	Duodenum
10	chr9:71790200-71792200	Enhancers	H9 Cell Line	embryonic stem cell
11	chr9:71790200-71792400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:71790200-71793400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr9:71790400-71791800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr9:71790400-71792200	Enhancers	Placenta	Placenta
15	chr9:71790400-71792800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:71790400-71793000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr9:71790400-71793200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr9:71790400-71795200	Enhancers	HUVEC	blood vessel
19	chr9:71790400-71795400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:71790400-71795400	Weak transcription	Pancreas	Pancrea
21	chr9:71790400-71795600	Weak transcription	Spleen	Spleen
22	chr9:71790400-71796800	Weak transcription	Esophagus	oesophagus
23	chr9:71790400-71832200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr9:71790400-71835600	Weak transcription	Colonic Mucosa	Colon
25	chr9:71790600-71791600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr9:71790600-71791800	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr9:71790600-71791800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr9:71790600-71792000	Weak transcription	Fetal Kidney	kidney
29	chr9:71790600-71792400	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr9:71790600-71792400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:71790600-71792400	Flanking Active TSS	NHEK	skin
32	chr9:71790600-71793000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr9:71790600-71793400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr9:71790600-71793600	Enhancers	H1 Cell Line	embryonic stem cell
35	chr9:71790600-71795200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr9:71790800-71791600	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr9:71790800-71791800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:71790800-71791800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr9:71790800-71792000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:71790800-71792200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr9:71790800-71792200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr9:71790800-71792400	Flanking Active TSS	GM12878-XiMat	blood
43	chr9:71790800-71793200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr9:71790800-71793400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr9:71790800-71793400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr9:71790800-71795000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr9:71790800-71797000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:71790800-71797000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr9:71790800-71800800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr9:71790800-71802200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links