Variant report

Variant	rs2498436
Chromosome Location	chr9:71790905-71790906
allele	A/G
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: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10735655	0.94[ASN][1000 genomes]
rs10781479	0.90[ASN][1000 genomes]
rs10869992	0.93[ASN][1000 genomes]
rs10869993	0.93[ASN][1000 genomes]
rs10869994	0.93[ASN][1000 genomes]
rs10869997	0.93[ASN][1000 genomes]
rs10870006	0.93[ASN][1000 genomes]
rs10870012	0.91[ASN][1000 genomes]
rs10870015	0.91[ASN][1000 genomes]
rs10870017	0.91[ASN][1000 genomes]
rs11145627	0.93[ASN][1000 genomes]
rs11145648	0.92[ASN][1000 genomes]
rs11145688	0.91[ASN][1000 genomes]
rs17062237	0.93[ASN][1000 genomes]
rs2309422	0.93[ASN][1000 genomes]
rs2309425	0.94[ASN][1000 genomes]
rs2309427	0.91[ASN][1000 genomes]
rs2486449	0.91[ASN][1000 genomes]
rs2993818	0.89[ASN][1000 genomes]
rs2993819	0.94[ASN][1000 genomes]
rs2993820	0.94[ASN][1000 genomes]
rs3002377	0.94[ASN][1000 genomes]
rs3002378	0.94[ASN][1000 genomes]
rs3002379	0.94[ASN][1000 genomes]
rs3002380	0.94[ASN][1000 genomes]
rs3002382	0.94[ASN][1000 genomes]
rs3750549	0.91[ASN][1000 genomes]
rs3927676	0.91[ASN][1000 genomes]
rs4338173	0.91[ASN][1000 genomes]
rs4576478	0.94[ASN][1000 genomes]
rs55641500	0.92[ASN][1000 genomes]
rs56226859	0.93[ASN][1000 genomes]
rs56312702	0.93[ASN][1000 genomes]
rs58264616	0.93[ASN][1000 genomes]
rs60785288	0.93[ASN][1000 genomes]
rs61074083	0.93[ASN][1000 genomes]
rs62567148	0.93[ASN][1000 genomes]
rs6560618	0.94[ASN][1000 genomes]
rs6560627	0.91[ASN][1000 genomes]
rs7020869	0.91[ASN][1000 genomes]
rs7038854	0.91[ASN][1000 genomes]
rs7041781	0.91[ASN][1000 genomes]
rs7045103	0.90[ASN][1000 genomes]
rs7048648	0.91[ASN][1000 genomes]
rs7350225	0.91[ASN][1000 genomes]
rs7850766	0.94[ASN][1000 genomes]
rs7861292	0.91[ASN][1000 genomes]
rs7864775	0.94[ASN][1000 genomes]
rs7873004	0.91[ASN][1000 genomes]
rs7874888	0.87[ASN][1000 genomes]
rs867346	0.92[ASN][1000 genomes]
rs884428	0.93[ASN][1000 genomes]
rs884429	0.93[ASN][1000 genomes]
rs9410783	0.91[ASN][1000 genomes]
rs9411195	0.96[ASN][1000 genomes]
rs9411200	0.94[ASN][1000 genomes]
rs946540	0.94[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2498436	TJP2	cis	Muscle Skeletal	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71788200-71797200	Enhancers	Stomach Mucosa	stomach
2	chr9:71788400-71791200	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr9:71788600-71791000	Active TSS	NHDF-Ad	bronchial
4	chr9:71788600-71791200	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr9:71788600-71791200	Active TSS	Brain Substantia Nigra	brain
6	chr9:71788600-71791400	Weak transcription	Small Intestine	intestine
7	chr9:71788800-71791000	Active TSS	Brain Hippocampus Middle	brain
8	chr9:71788800-71791000	Active TSS	Stomach Smooth Muscle	stomach
9	chr9:71788800-71791400	Active TSS	Placenta Amnion	Placenta Amnion
10	chr9:71788800-71792000	Active TSS	Liver	Liver
11	chr9:71789400-71791600	Flanking Active TSS	HepG2	liver
12	chr9:71789400-71792400	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr9:71789600-71791000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr9:71789600-71791000	Flanking Active TSS	Fetal Heart	heart
15	chr9:71789600-71791000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr9:71789600-71792000	Weak transcription	Gastric	stomach
17	chr9:71789800-71792400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:71790000-71791800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr9:71790000-71792000	Enhancers	Hela-S3	cervix
20	chr9:71790200-71791000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
21	chr9:71790200-71791200	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr9:71790200-71791400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr9:71790200-71791400	Flanking Active TSS	K562	blood
24	chr9:71790200-71791600	Enhancers	Duodenum Mucosa	Duodenum
25	chr9:71790200-71792200	Enhancers	H9 Cell Line	embryonic stem cell
26	chr9:71790200-71792400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:71790200-71793400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr9:71790400-71791000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:71790400-71791000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:71790400-71791000	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr9:71790400-71791000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:71790400-71791000	Flanking Active TSS	HMEC	breast
33	chr9:71790400-71791200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr9:71790400-71791200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr9:71790400-71791200	Weak transcription	Fetal Intestine Small	intestine
36	chr9:71790400-71791200	Enhancers	Psoas Muscle	Psoas
37	chr9:71790400-71791200	Flanking Active TSS	NH-A	brain
38	chr9:71790400-71791200	Flanking Active TSS	NHLF	lung
39	chr9:71790400-71791200	Flanking Active TSS	Osteobl	bone
40	chr9:71790400-71791400	Weak transcription	Fetal Intestine Large	intestine
41	chr9:71790400-71791400	Enhancers	Left Ventricle	heart
42	chr9:71790400-71791800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr9:71790400-71792200	Enhancers	Placenta	Placenta
44	chr9:71790400-71792800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr9:71790400-71793000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr9:71790400-71793200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr9:71790400-71795200	Enhancers	HUVEC	blood vessel
48	chr9:71790400-71795400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr9:71790400-71795400	Weak transcription	Pancreas	Pancrea
50	chr9:71790400-71795600	Weak transcription	Spleen	Spleen

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