Variant report

Variant	rs10126006
Chromosome Location	chr9:71674125-71674126
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71671960..71674521-chr9:71677007..71679466,3	K562	blood:
2	chr9:71672508..71675484-chr9:71734022..71736530,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119139	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1045632	0.82[ASN][1000 genomes]
rs10747003	0.82[ASN][1000 genomes]
rs10781379	0.90[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs10869821	0.84[ASN][1000 genomes]
rs10869823	0.83[ASN][1000 genomes]
rs10890	0.90[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs11145043	0.84[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11145070	0.82[ASN][1000 genomes]
rs11145072	0.83[ASN][1000 genomes]
rs11145106	0.82[ASN][1000 genomes]
rs11789036	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12348477	0.80[ASN][1000 genomes]
rs1411675	0.90[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1411676	0.90[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1984002	0.88[ASN][1000 genomes]
rs1984003	0.86[ASN][1000 genomes]
rs1984004	0.90[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2309393	0.92[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2309394	0.91[CHB][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes]
rs2498434	0.81[CHB][hapmap]
rs2871219	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2871220	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3763608	0.84[CEU][hapmap]
rs3793456	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3793457	0.91[CHB][hapmap];0.88[AMR][1000 genomes]
rs3793458	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3793461	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3793465	0.88[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3793466	0.90[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3793467	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3829062	0.91[CHB][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap]
rs4596713	0.82[ASN][1000 genomes]
rs4744806	0.88[ASN][1000 genomes]
rs4744808	0.90[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs4745543	0.84[CEU][hapmap]
rs4745577	0.90[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs4745581	0.90[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs4745585	0.82[ASN][1000 genomes]
rs57561255	0.83[ASN][1000 genomes]
rs6560545	0.82[ASN][1000 genomes]
rs6560546	0.82[ASN][1000 genomes]
rs7024295	0.83[ASN][1000 genomes]
rs7028835	0.81[ASN][1000 genomes]
rs7039631	0.83[ASN][1000 genomes]
rs7041324	0.81[ASN][1000 genomes]
rs7047274	0.91[CHB][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes]
rs7849347	0.84[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7855905	0.84[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7858249	0.87[ASN][1000 genomes]
rs7858407	0.87[ASN][1000 genomes]
rs7858657	0.88[ASN][1000 genomes]
rs7859021	0.82[ASN][1000 genomes]
rs7865353	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7865854	0.88[ASN][1000 genomes]
rs7866067	0.87[ASN][1000 genomes]
rs7870727	0.88[ASN][1000 genomes]
rs7871596	0.91[CHB][hapmap];0.84[TSI][hapmap]
rs7874105	0.84[ASN][1000 genomes]
rs7874989	0.87[ASN][1000 genomes]
rs7875564	0.87[ASN][1000 genomes]
rs7875659	0.90[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7875693	0.84[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9314854	0.90[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9411170	0.86[CHB][hapmap];0.80[MEX][hapmap]
rs9411171	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	nsv1035268	chr9:71665139-71691673	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10126006	TJP2	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71651800-71680600	Weak transcription	HSMMtube	muscle
2	chr9:71652000-71680600	Weak transcription	Brain Angular Gyrus	brain
3	chr9:71652000-71680800	Weak transcription	Primary B cells from cord blood	blood
4	chr9:71659600-71689800	Weak transcription	Colonic Mucosa	Colon
5	chr9:71659800-71683000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:71659800-71683000	Weak transcription	Psoas Muscle	Psoas
7	chr9:71659800-71685200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr9:71660000-71679000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr9:71660000-71680800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr9:71660000-71682000	Weak transcription	NHLF	lung
11	chr9:71660000-71684400	Weak transcription	Small Intestine	intestine
12	chr9:71660000-71689400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr9:71661000-71675600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:71661200-71684800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr9:71662000-71679800	Weak transcription	Fetal Kidney	kidney
16	chr9:71662400-71675400	Weak transcription	Fetal Heart	heart
17	chr9:71662800-71686400	Weak transcription	Fetal Brain Female	brain
18	chr9:71664000-71674600	Weak transcription	HUVEC	blood vessel
19	chr9:71664000-71675400	Weak transcription	Brain Hippocampus Middle	brain
20	chr9:71664000-71675600	Weak transcription	Brain Substantia Nigra	brain
21	chr9:71664000-71675600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr9:71664000-71682000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr9:71664200-71675600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr9:71664200-71679400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr9:71664200-71680800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr9:71664200-71681400	Weak transcription	Right Ventricle	heart
27	chr9:71664200-71691200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:71664400-71675200	Weak transcription	Pancreas	Pancrea
29	chr9:71664400-71675600	Weak transcription	Lung	lung
30	chr9:71664400-71675600	Weak transcription	Spleen	Spleen
31	chr9:71664400-71675800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:71664400-71675800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:71664400-71675800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr9:71664400-71678800	Weak transcription	Aorta	Aorta
35	chr9:71664400-71680400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr9:71664400-71680600	Weak transcription	A549	lung
37	chr9:71664400-71680800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr9:71664400-71680800	Weak transcription	Esophagus	oesophagus
39	chr9:71664400-71681400	Weak transcription	Gastric	stomach
40	chr9:71664400-71693600	Weak transcription	HMEC	breast
41	chr9:71664600-71680400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:71665000-71675800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr9:71665000-71676000	Weak transcription	Ovary	ovary
44	chr9:71665000-71680400	Weak transcription	Placenta	Placenta
45	chr9:71665200-71679800	Weak transcription	Osteobl	bone
46	chr9:71665200-71680600	Weak transcription	NH-A	brain
47	chr9:71668000-71674200	Strong transcription	Fetal Muscle Leg	muscle
48	chr9:71668000-71674200	Strong transcription	HepG2	liver
49	chr9:71668000-71675400	Strong transcription	Primary T cells from cord blood	blood
50	chr9:71668400-71676400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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