Variant report

Variant	rs6486361
Chromosome Location	chr11:9473074-9473075
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9469128..9470707-chr11:9471255..9473925,2	K562	blood:
2	chr11:9471254..9473102-chr11:9481139..9483040,2	MCF-7	breast:
3	chr11:9471434..9473204-chr11:9611341..9613094,2	K562	blood:
4	chr11:9469838..9473131-chr11:9479666..9482580,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166478	Chromatin interaction
ENSG00000268403	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1020621	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1020622	1.00[ASN][1000 genomes]
rs10437665	0.89[GIH][hapmap];0.81[JPT][hapmap]
rs10743107	0.90[ASN][1000 genomes]
rs10770028	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10770029	0.89[ASN][1000 genomes]
rs10770032	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10770033	1.00[ASN][1000 genomes]
rs10770034	0.83[ASN][1000 genomes]
rs10840228	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10840234	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs10840235	0.84[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10840236	0.93[ASN][1000 genomes]
rs10840237	0.98[ASN][1000 genomes]
rs10840238	0.99[ASN][1000 genomes]
rs10840241	0.87[ASN][1000 genomes]
rs10840243	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10840244	0.82[ASN][1000 genomes]
rs10840245	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10840247	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10840249	0.81[ASN][1000 genomes]
rs10840253	0.86[JPT][hapmap]
rs11042328	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11042329	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs11042348	0.97[ASN][1000 genomes]
rs11042349	0.94[ASN][1000 genomes]
rs11042350	0.99[ASN][1000 genomes]
rs11042353	1.00[ASN][1000 genomes]
rs11042355	1.00[ASN][1000 genomes]
rs11042356	1.00[ASN][1000 genomes]
rs11042366	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11042374	0.84[ASN][1000 genomes]
rs11042377	0.86[ASN][1000 genomes]
rs11042395	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs11826606	0.94[ASN][1000 genomes]
rs12225755	0.94[ASN][1000 genomes]
rs12271897	0.99[ASN][1000 genomes]
rs12282176	1.00[ASN][1000 genomes]
rs12296039	0.96[ASN][1000 genomes]
rs12792161	0.85[ASN][1000 genomes]
rs12795344	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12797567	0.97[ASN][1000 genomes]
rs12799672	0.87[ASN][1000 genomes]
rs12800802	0.99[ASN][1000 genomes]
rs12806418	0.85[ASN][1000 genomes]
rs1377667	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1470896	0.82[ASN][1000 genomes]
rs1543	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1968717	0.86[ASN][1000 genomes]
rs2278900	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2290423	0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2290424	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2290425	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs35781320	0.97[ASN][1000 genomes]
rs3763877	0.82[ASN][1000 genomes]
rs41369549	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4625466	0.95[JPT][hapmap]
rs4810	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4910048	0.81[JPT][hapmap]
rs4910053	0.95[JPT][hapmap]
rs4910468	0.82[ASN][1000 genomes]
rs6486306	0.86[ASN][1000 genomes]
rs6486307	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6486359	1.00[ASN][1000 genomes]
rs6486394	0.88[ASW][hapmap];0.90[CEU][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67548305	1.00[ASN][1000 genomes]
rs68060819	0.82[ASN][1000 genomes]
rs7102473	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7103931	0.88[ASN][1000 genomes]
rs7104568	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7114824	0.92[ASN][1000 genomes]
rs7122252	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7122499	0.88[ASN][1000 genomes]
rs723297	0.88[ASW][hapmap];0.90[CEU][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs727405	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs729313	0.88[ASW][hapmap];0.86[CEU][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7395411	0.98[ASN][1000 genomes]
rs7483667	0.84[ASN][1000 genomes]
rs7926589	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7927350	0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7928823	0.85[ASN][1000 genomes]
rs7928945	0.87[ASN][1000 genomes]
rs7932192	0.89[ASN][1000 genomes]
rs7933621	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7944435	0.89[ASN][1000 genomes]
rs7944578	0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7949973	1.00[ASN][1000 genomes]
rs8785	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9667574	0.92[ASN][1000 genomes]
rs972594	0.88[ASW][hapmap];0.86[CEU][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9787851	0.83[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	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1055078	chr11:9252857-9538877	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv1039537	chr11:9455387-9535970	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv825762	chr11:9470175-9479714	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6486361	IPO7	Cis_1M	lymphoblastoid	RTeQTL
rs6486361	OR56A1	cis	cerebellum	SCAN
rs6486361	GVIN1	cis	parietal	SCAN
rs6486361	IPO7	cis	multi-tissue	Pritchard
rs6486361	SNORA23	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9452800-9480000	Weak transcription	Fetal Brain Male	brain
2	chr11:9457800-9480600	Weak transcription	Psoas Muscle	Psoas
3	chr11:9461800-9474800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:9462200-9481000	Weak transcription	NHLF	lung
5	chr11:9463400-9481000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr11:9463800-9481000	Weak transcription	NHDF-Ad	bronchial
7	chr11:9464800-9480800	Weak transcription	HSMMtube	muscle
8	chr11:9465000-9474400	Weak transcription	Colon Smooth Muscle	Colon
9	chr11:9465000-9480800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:9465000-9480800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr11:9465000-9481000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr11:9465200-9476000	Weak transcription	Aorta	Aorta
13	chr11:9465200-9481000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr11:9465200-9481200	Weak transcription	Ovary	ovary
15	chr11:9465400-9481000	Weak transcription	Brain Substantia Nigra	brain
16	chr11:9465400-9481000	Weak transcription	K562	blood
17	chr11:9465800-9480600	Weak transcription	Esophagus	oesophagus
18	chr11:9465800-9481000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr11:9466200-9473400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr11:9466400-9480600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr11:9466600-9475200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:9466600-9480800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr11:9466800-9480800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr11:9466800-9481000	Weak transcription	Fetal Lung	lung
25	chr11:9467000-9473400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr11:9467000-9480800	Weak transcription	Lung	lung
27	chr11:9467400-9480800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr11:9468000-9481000	Weak transcription	Fetal Heart	heart
29	chr11:9468000-9481000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr11:9468000-9481000	Weak transcription	NH-A	brain
31	chr11:9468200-9481000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr11:9468600-9473200	Weak transcription	Liver	Liver
33	chr11:9468600-9473600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr11:9470200-9473200	Weak transcription	Hela-S3	cervix
35	chr11:9470200-9475000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr11:9470200-9476000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr11:9470200-9480800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr11:9470200-9480800	Weak transcription	Left Ventricle	heart
39	chr11:9470200-9480800	Weak transcription	HSMM	muscle
40	chr11:9470200-9480800	Weak transcription	NHEK	skin
41	chr11:9470200-9481000	Weak transcription	A549	lung
42	chr11:9470200-9481000	Weak transcription	HUVEC	blood vessel
43	chr11:9470200-9481200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:9470400-9480800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr11:9470400-9480800	Weak transcription	HMEC	breast
46	chr11:9470400-9481000	Weak transcription	Osteobl	bone
47	chr11:9470600-9480800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr11:9470800-9480800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr11:9471000-9473600	Weak transcription	Fetal Stomach	stomach
50	chr11:9471000-9480800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links