Variant report

Variant	rs10870015
Chromosome Location	chr9:71818432-71818433
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:71818348-71818539	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71782838..71785289-chr9:71817558..71819101,2	MCF-7	breast:
2	chr9:71813787..71816021-chr9:71816458..71819040,2	K562	blood:

Variant related genes	Relation type
TJP2	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10735655	0.94[ASN][1000 genomes]
rs10781479	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10869992	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10869993	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10869994	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10869997	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10870006	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10870012	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10870017	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11145627	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11145648	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11145688	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17062237	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2309422	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2309425	0.94[ASN][1000 genomes]
rs2309427	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2486449	0.97[ASN][1000 genomes]
rs2498436	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	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3927676	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4338173	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4576478	0.94[ASN][1000 genomes]
rs55641500	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56226859	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56312702	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58264616	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60785288	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61074083	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62567148	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6560618	0.94[ASN][1000 genomes]
rs6560627	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7020869	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038854	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041781	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7045103	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7048648	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7350225	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7850766	0.94[ASN][1000 genomes]
rs7861292	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7864775	0.94[ASN][1000 genomes]
rs7873004	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7874888	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs867346	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs884428	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs884429	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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:20 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
rs10870015	TJP2	cis	Whole Blood	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71790400-71832200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr9:71790400-71835600	Weak transcription	Colonic Mucosa	Colon
3	chr9:71797200-71832000	Weak transcription	Esophagus	oesophagus
4	chr9:71804000-71831800	Weak transcription	Aorta	Aorta
5	chr9:71806600-71819000	Weak transcription	Fetal Kidney	kidney
6	chr9:71807400-71832200	Weak transcription	Primary T cells from cord blood	blood
7	chr9:71807800-71842800	Weak transcription	Small Intestine	intestine
8	chr9:71808000-71819200	Weak transcription	NHLF	lung
9	chr9:71808200-71819000	Weak transcription	Fetal Stomach	stomach
10	chr9:71808200-71819200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr9:71810400-71832400	Weak transcription	GM12878-XiMat	blood
12	chr9:71810600-71818800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr9:71811000-71819000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:71811200-71822400	Weak transcription	Pancreas	Pancrea
15	chr9:71811600-71819400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr9:71813000-71819000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:71813400-71819000	Weak transcription	Placenta	Placenta
18	chr9:71813600-71819200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:71813800-71818800	Weak transcription	Brain Anterior Caudate	brain
20	chr9:71814000-71818800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr9:71814800-71820000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:71814800-71820000	Weak transcription	Psoas Muscle	Psoas
23	chr9:71815000-71818800	Weak transcription	Fetal Lung	lung
24	chr9:71815000-71819000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr9:71815000-71819000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr9:71815000-71819200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr9:71815000-71819400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr9:71815000-71819800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr9:71815000-71830000	Weak transcription	HUVEC	blood vessel
30	chr9:71815200-71832200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr9:71815400-71818600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:71815400-71818800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:71815400-71818800	Weak transcription	Right Atrium	heart
34	chr9:71815400-71818800	Weak transcription	K562	blood
35	chr9:71815400-71819000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr9:71815400-71819000	Weak transcription	Stomach Mucosa	stomach
37	chr9:71815400-71819200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr9:71815400-71830000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr9:71815600-71818800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr9:71815600-71818800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr9:71815600-71819000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr9:71815600-71819200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr9:71815600-71819400	Weak transcription	Adipose Nuclei	Adipose
44	chr9:71815600-71819400	Weak transcription	HSMM	muscle
45	chr9:71815600-71820000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr9:71815800-71819000	Weak transcription	NHEK	skin
47	chr9:71815800-71819200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr9:71816000-71818800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr9:71816000-71819000	Weak transcription	Brain Angular Gyrus	brain
50	chr9:71816000-71819000	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links