Variant report

Variant	rs953588
Chromosome Location	chr9:71704827-71704828
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71704008..71706268-chr9:71714594..71717470,2	MCF-7	breast:
2	chr9:71704381..71705131-chr9:71714234..71715231,2	MCF-7	breast:
3	chr9:71699941..71701534-chr9:71703830..71705802,2	MCF-7	breast:
4	chr9:71704193..71706680-chr9:71707400..71709954,2	K562	blood:

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10117212	0.99[ASN][1000 genomes]
rs10125005	0.91[ASN][1000 genomes]
rs10126006	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs1045632	0.91[ASN][1000 genomes]
rs10747003	0.91[ASN][1000 genomes]
rs10781379	0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs10781392	0.86[ASN][1000 genomes]
rs10781394	1.00[ASN][1000 genomes]
rs10869821	0.88[ASN][1000 genomes]
rs10869823	0.90[ASN][1000 genomes]
rs10869824	0.83[ASN][1000 genomes]
rs10890	0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs11145043	0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.84[MKK][hapmap];0.85[ASN][1000 genomes]
rs11145069	0.83[ASN][1000 genomes]
rs11145070	0.88[ASN][1000 genomes]
rs11145072	0.90[ASN][1000 genomes]
rs11145106	0.91[ASN][1000 genomes]
rs11789036	0.81[ASN][1000 genomes]
rs12338940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348477	0.89[ASN][1000 genomes]
rs1411675	0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs1411676	0.95[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs1984002	0.85[ASN][1000 genomes]
rs1984003	0.83[ASN][1000 genomes]
rs1984004	0.95[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2309393	0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs2498430	0.82[CHB][hapmap]
rs2498431	0.82[CHB][hapmap]
rs2498433	0.82[CHB][hapmap]
rs2498434	0.86[CHB][hapmap]
rs3793456	0.86[CHB][hapmap]
rs3793461	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs3793465	0.95[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.84[MKK][hapmap]
rs3793466	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs3793467	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs3829064	0.86[CHB][hapmap]
rs4596713	0.91[ASN][1000 genomes]
rs4744806	0.85[ASN][1000 genomes]
rs4744807	0.82[CHB][hapmap]
rs4744808	0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs4745577	0.95[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs4745580	0.82[CHB][hapmap]
rs4745581	0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs4745585	0.91[ASN][1000 genomes]
rs57561255	0.90[ASN][1000 genomes]
rs6560545	0.91[ASN][1000 genomes]
rs6560546	0.91[ASN][1000 genomes]
rs7024295	0.90[ASN][1000 genomes]
rs7028835	0.89[ASN][1000 genomes]
rs7035156	0.81[ASN][1000 genomes]
rs7039631	0.90[ASN][1000 genomes]
rs7041324	0.89[ASN][1000 genomes]
rs7849347	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7855905	0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.84[MKK][hapmap];0.91[ASN][1000 genomes]
rs7858249	0.85[ASN][1000 genomes]
rs7858407	0.84[ASN][1000 genomes]
rs7858657	0.85[ASN][1000 genomes]
rs7859021	0.91[ASN][1000 genomes]
rs7861997	0.82[CHB][hapmap]
rs7865854	0.85[ASN][1000 genomes]
rs7866067	0.85[ASN][1000 genomes]
rs7870295	0.82[CHB][hapmap]
rs7870727	0.85[ASN][1000 genomes]
rs7874105	0.88[ASN][1000 genomes]
rs7874989	0.85[ASN][1000 genomes]
rs7875564	0.85[ASN][1000 genomes]
rs7875659	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7875693	0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.92[MKK][hapmap];0.85[ASN][1000 genomes]
rs9314854	0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs944348	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:34 , 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	nsv466393	chr9:71453443-71704827	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS 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	10 gene(s)	inside rSNPs	diseases
10	nsv614547	chr9:71453443-71704827	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	nsv893426	chr9:71659280-71719618	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
27	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
28	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
29	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
30	esv2761531	chr9:71684369-71718459	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
31	nsv1047528	chr9:71686476-71717502	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
32	nsv1042844	chr9:71686476-71718447	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
33	nsv1051764	chr9:71689756-71716055	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
34	nsv6549	chr9:71701393-71708756	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs953588	TJP2	cis	Whole Blood	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71684800-71705800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:71688800-71709200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:71694200-71711800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:71701000-71705600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:71701200-71705200	Weak transcription	Adipose Nuclei	Adipose
6	chr9:71701200-71705600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:71701400-71714400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:71701600-71705400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:71701600-71709400	Weak transcription	Gastric	stomach
10	chr9:71701800-71735200	Weak transcription	Primary T cells from cord blood	blood
11	chr9:71702000-71716800	Weak transcription	Fetal Heart	heart
12	chr9:71702200-71705600	Weak transcription	Fetal Lung	lung
13	chr9:71702200-71708200	Weak transcription	Pancreas	Pancrea
14	chr9:71702400-71707600	Weak transcription	HepG2	liver
15	chr9:71702400-71711200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:71702800-71705200	Weak transcription	Fetal Stomach	stomach
17	chr9:71704000-71705000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:71704000-71705400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr9:71704000-71705400	Enhancers	Placenta	Placenta
20	chr9:71704000-71706000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:71704200-71705400	Enhancers	H9 Cell Line	embryonic stem cell
22	chr9:71704200-71705800	Weak transcription	NHEK	skin
23	chr9:71704400-71705200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr9:71704400-71705200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr9:71704400-71705400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr9:71704400-71705800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr9:71704400-71705800	Enhancers	Stomach Mucosa	stomach
28	chr9:71704400-71707400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr9:71704600-71705200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
30	chr9:71704600-71705200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr9:71704600-71705200	Enhancers	Left Ventricle	heart
32	chr9:71704600-71705400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:71704600-71705400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr9:71704600-71705400	Enhancers	Fetal Intestine Small	intestine
35	chr9:71704600-71705800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr9:71704600-71705800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:71704600-71705800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr9:71704600-71705800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr9:71704600-71705800	Enhancers	Lung	lung
40	chr9:71704600-71706600	Enhancers	HUVEC	blood vessel
41	chr9:71704800-71705400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr9:71704800-71705800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr9:71704800-71705800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr9:71704800-71706200	Enhancers	Fetal Kidney	kidney
45	chr9:71704800-71706400	Enhancers	Small Intestine	intestine
46	chr9:71704800-71708600	Weak transcription	Fetal Intestine Large	intestine
47	chr9:71704800-71708800	Weak transcription	Right Ventricle	heart

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