Variant report

Variant	rs7131597
Chromosome Location	chr11:120303939-120303940
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:120302832..120305413-chr11:120306249..120308301,2	K562	blood:
2	chr11:120208182..120211778-chr11:120301083..120304985,6	K562	blood:
3	chr11:120206012..120208524-chr11:120302971..120304695,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196914	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10502235	0.90[JPT][hapmap]
rs10750172	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10750173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10750174	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10790378	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10790380	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10790382	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10790383	0.93[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10892562	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10892563	0.92[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10892564	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10892566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10892567	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10892570	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10892574	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10892576	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10892578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10892582	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11217821	0.88[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs11217840	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11217841	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11217852	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11217874	0.84[JPT][hapmap]
rs11217875	0.89[JPT][hapmap]
rs11217887	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11600703	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11601535	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11827818	0.84[JPT][hapmap]
rs12417256	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12420378	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12787285	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12794946	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12806740	0.88[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs1373270	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1892894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1893261	0.88[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs2276035	0.84[JPT][hapmap]
rs2305008	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305010	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3809059	0.81[JPT][hapmap]
rs4381380	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4539328	0.81[AMR][1000 genomes]
rs4936517	0.84[EUR][1000 genomes]
rs4938799	0.92[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs4938801	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4938804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4938805	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4938806	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4938807	0.90[JPT][hapmap]
rs4938808	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs496248	0.81[JPT][hapmap]
rs632137	0.81[JPT][hapmap]
rs6589810	0.85[EUR][1000 genomes]
rs6589811	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6589812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6589813	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7101415	0.85[EUR][1000 genomes]
rs7104639	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7107211	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7115714	0.91[EUR][1000 genomes]
rs7117063	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7117321	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7118391	0.98[GIH][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7121779	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7126328	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7129944	0.90[JPT][hapmap]
rs7131046	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs723937	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7478880	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7924772	0.84[EUR][1000 genomes]
rs7924963	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7924975	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7932037	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7933086	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7937612	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7939137	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7948928	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7951250	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs894839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9633919	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9633950	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv529003	chr11:120209386-120355230	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1051672	chr11:120238962-120314178	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1051783	chr11:120246224-120314178	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7131597	ARHGEF12	cis	cerebellum	SCAN
rs7131597	TMEM136	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120272200-120315600	Weak transcription	Brain Germinal Matrix	brain
2	chr11:120272200-120315800	Weak transcription	Brain Hippocampus Middle	brain
3	chr11:120272400-120320600	Weak transcription	Psoas Muscle	Psoas
4	chr11:120275600-120322200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:120275800-120314000	Weak transcription	Right Ventricle	heart
6	chr11:120277600-120319800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:120285600-120319800	Weak transcription	Gastric	stomach
8	chr11:120288400-120305800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:120288600-120309600	Weak transcription	Aorta	Aorta
10	chr11:120290000-120308200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr11:120290400-120313400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:120291800-120319200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr11:120292000-120315400	Weak transcription	Colonic Mucosa	Colon
14	chr11:120293000-120309000	Weak transcription	Fetal Stomach	stomach
15	chr11:120294000-120316000	Weak transcription	Primary B cells from cord blood	blood
16	chr11:120295400-120312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:120295400-120318600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr11:120296000-120308400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr11:120296000-120309200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr11:120296000-120312400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr11:120296000-120315800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr11:120296000-120316200	Weak transcription	Esophagus	oesophagus
23	chr11:120296000-120316400	Weak transcription	Lung	lung
24	chr11:120296000-120317600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr11:120296200-120308400	Weak transcription	Adipose Nuclei	Adipose
26	chr11:120296200-120315400	Weak transcription	Fetal Brain Male	brain
27	chr11:120296400-120308400	Weak transcription	Fetal Muscle Leg	muscle
28	chr11:120296400-120308400	Weak transcription	HepG2	liver
29	chr11:120297000-120305600	Strong transcription	Placenta	Placenta
30	chr11:120298600-120305200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr11:120298800-120304200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:120299600-120308200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr11:120300000-120304600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr11:120300600-120308400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr11:120300600-120312000	Strong transcription	Liver	Liver
36	chr11:120300800-120306400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr11:120300800-120308400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr11:120301200-120304600	Strong transcription	Fetal Lung	lung
39	chr11:120301400-120308000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr11:120301400-120355200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr11:120302000-120304000	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr11:120302000-120304400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr11:120302400-120304000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:120302400-120304000	Enhancers	NHLF	lung
45	chr11:120302400-120304400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:120302600-120304000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr11:120302600-120308000	Weak transcription	Fetal Intestine Large	intestine
48	chr11:120302600-120308200	Weak transcription	Brain Angular Gyrus	brain
49	chr11:120302600-120310000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:120302600-120312400	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links