Variant report

Variant	rs7925889
Chromosome Location	chr11:10048319-10048320
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10160247	0.80[JPT][hapmap]
rs10160669	0.80[JPT][hapmap]
rs10500716	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10500719	0.80[JPT][hapmap]
rs10500720	0.84[JPT][hapmap]
rs10500721	0.83[CHB][hapmap]
rs10500722	0.81[CHD][hapmap];0.80[JPT][hapmap]
rs11042575	0.94[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap]
rs11042586	0.88[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs11042656	0.80[JPT][hapmap]
rs11042664	0.80[JPT][hapmap]
rs11042666	0.80[JPT][hapmap]
rs11821308	0.83[CHB][hapmap]
rs12274104	0.80[JPT][hapmap]
rs12278680	0.80[JPT][hapmap]
rs12278735	0.80[JPT][hapmap]
rs12281526	0.80[JPT][hapmap]
rs12286927	0.80[JPT][hapmap]
rs12287386	0.80[JPT][hapmap]
rs12288200	0.80[JPT][hapmap]
rs12288275	0.80[JPT][hapmap]
rs12288486	0.80[JPT][hapmap]
rs12288654	0.80[JPT][hapmap]
rs1442736	0.80[JPT][hapmap]
rs16907329	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs16907334	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs16907407	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs16907410	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16907417	0.94[CHB][hapmap]
rs16907462	0.80[JPT][hapmap]
rs16907481	0.80[JPT][hapmap]
rs16907493	0.80[JPT][hapmap]
rs16907504	0.80[JPT][hapmap]
rs16907533	0.80[JPT][hapmap]
rs16907561	0.80[JPT][hapmap]
rs16907568	0.80[JPT][hapmap]
rs1822295	0.80[JPT][hapmap]
rs1867137	0.80[JPT][hapmap]
rs1867138	0.80[JPT][hapmap]
rs2069214	0.80[JPT][hapmap]
rs2119991	0.80[JPT][hapmap]
rs2278630	0.80[JPT][hapmap]
rs2278632	0.80[JPT][hapmap]
rs2278633	0.83[JPT][hapmap]
rs2278634	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs2403261	0.88[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs2403267	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2896513	0.88[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2896514	0.94[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2896515	0.84[ASN][1000 genomes]
rs2896517	0.88[ASN][1000 genomes]
rs3178898	0.80[JPT][hapmap]
rs4910090	0.93[CHB][hapmap];0.85[JPT][hapmap]
rs4910091	0.84[ASN][1000 genomes]
rs4910092	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs56850765	0.86[ASN][1000 genomes]
rs57180563	0.83[ASN][1000 genomes]
rs59479500	0.85[ASN][1000 genomes]
rs61877018	0.92[ASN][1000 genomes]
rs61877040	0.88[ASN][1000 genomes]
rs61877043	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs61877045	0.86[ASN][1000 genomes]
rs6483969	0.85[JPT][hapmap]
rs67404901	0.82[ASN][1000 genomes]
rs7103902	1.00[CHB][hapmap]
rs7106234	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7107302	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7107916	1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs7121157	0.84[ASN][1000 genomes]
rs7124925	0.84[JPT][hapmap]
rs7128234	0.88[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7129047	0.80[JPT][hapmap]
rs7130610	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs713402	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs721008	0.80[JPT][hapmap]
rs7926141	0.84[ASN][1000 genomes]
rs7932484	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[ASN][1000 genomes]
rs7935297	0.97[ASN][1000 genomes]
rs7936461	1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7938543	0.80[JPT][hapmap]
rs7940348	0.92[ASN][1000 genomes]
rs7946649	0.80[JPT][hapmap]
rs9645625	0.88[JPT][hapmap]
rs9888170	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv896989	chr11:9951968-10059623	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv553475	chr11:10019879-10059623	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv553476	chr11:10024311-10117435	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9981400-10051600	Weak transcription	Aorta	Aorta
2	chr11:9985800-10049000	Weak transcription	Left Ventricle	heart
3	chr11:9991200-10060000	Weak transcription	Colon Smooth Muscle	Colon
4	chr11:10001400-10066200	Weak transcription	Pancreas	Pancrea
5	chr11:10004200-10048600	Weak transcription	Brain Angular Gyrus	brain
6	chr11:10010600-10051200	Weak transcription	Ovary	ovary
7	chr11:10012600-10049000	Weak transcription	Fetal Kidney	kidney
8	chr11:10024800-10054000	Weak transcription	Hela-S3	cervix
9	chr11:10030600-10051400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:10030600-10054000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:10030600-10065800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:10032800-10049200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr11:10035200-10065800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr11:10035400-10051200	Weak transcription	Psoas Muscle	Psoas
15	chr11:10035800-10052800	Weak transcription	Spleen	Spleen
16	chr11:10036000-10049000	Weak transcription	Placenta	Placenta
17	chr11:10036000-10055600	Weak transcription	NHEK	skin
18	chr11:10036200-10062800	Weak transcription	Adipose Nuclei	Adipose
19	chr11:10037600-10049400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:10040400-10065800	Weak transcription	HSMM	muscle
21	chr11:10040600-10049400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr11:10042000-10048800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr11:10042000-10052200	Weak transcription	Esophagus	oesophagus
24	chr11:10042000-10052800	Weak transcription	Lung	lung
25	chr11:10042000-10053400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr11:10042000-10055800	Weak transcription	HMEC	breast
27	chr11:10042200-10048400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:10042200-10049400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr11:10042200-10049600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr11:10042200-10054800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:10042200-10064400	Weak transcription	Fetal Intestine Small	intestine
32	chr11:10042200-10066000	Weak transcription	Fetal Muscle Leg	muscle
33	chr11:10042200-10066000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr11:10042200-10066200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr11:10042400-10048800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr11:10042600-10066000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr11:10042800-10054200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:10043400-10049400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr11:10043400-10051400	Weak transcription	Primary B cells from cord blood	blood
40	chr11:10043400-10051800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr11:10043400-10052000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr11:10043400-10065600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr11:10043600-10049000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:10043600-10049000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr11:10043600-10049000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr11:10043600-10049200	Weak transcription	Fetal Intestine Large	intestine
47	chr11:10043600-10050200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr11:10043800-10049000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr11:10043800-10049400	Weak transcription	Fetal Lung	lung
50	chr11:10043800-10054400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links