Variant report

Variant	rs7311008
Chromosome Location	chr12:56565392-56565393
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56510860..56512440-chr12:56563856..56566827,2	MCF-7	breast:
2	chr12:56508092..56528020-chr12:56536122..56568603,201	MCF-7	breast:
3	chr12:56562450..56567613-chr12:56569949..56573416,6	K562	blood:
4	chr12:56496158..56498229-chr12:56565147..56567681,2	MCF-7	breast:
5	chr12:56565316..56568211-chr12:56578622..56581281,2	K562	blood:
6	chr1:2344307..2345101-chr12:56564806..56565759,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000170515	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000139613	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10747763	1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10876878	0.95[ASN][1000 genomes]
rs11171745	0.82[GIH][hapmap];0.88[MEX][hapmap]
rs11171752	0.84[ASN][1000 genomes]
rs11171772	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11171773	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11171777	1.00[JPT][hapmap]
rs11834728	1.00[JPT][hapmap]
rs12229022	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12320265	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1274298	1.00[GIH][hapmap]
rs1274494	1.00[CHD][hapmap];0.80[MKK][hapmap]
rs1274502	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1274503	0.95[ASN][1000 genomes]
rs12810816	1.00[GIH][hapmap]
rs1290898	0.86[TSI][hapmap]
rs1405859	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1689512	0.82[GIH][hapmap];0.88[MEX][hapmap]
rs17118313	1.00[GIH][hapmap]
rs17118317	0.82[GIH][hapmap]
rs17118333	1.00[JPT][hapmap]
rs2271190	1.00[JPT][hapmap]
rs2271192	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[ASN][1000 genomes]
rs2456972	1.00[CHD][hapmap]
rs2463365	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2629451	0.95[ASN][1000 genomes]
rs2629453	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2640569	0.82[GIH][hapmap];0.88[MEX][hapmap]
rs2695783	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2695784	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2930788	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2950573	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3759096	1.00[JPT][hapmap]
rs3802996	1.00[JPT][hapmap]
rs3809130	1.00[JPT][hapmap]
rs4759218	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58009483	0.95[ASN][1000 genomes]
rs59053322	0.95[ASN][1000 genomes]
rs59078852	0.95[ASN][1000 genomes]
rs59966703	0.95[ASN][1000 genomes]
rs61939011	0.95[ASN][1000 genomes]
rs6581091	1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs703823	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7489249	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs772922	1.00[CHD][hapmap]
rs773120	1.00[GIH][hapmap]
rs773121	1.00[GIH][hapmap]
rs773122	1.00[GIH][hapmap]
rs773643	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs773649	0.92[GIH][hapmap]
rs773654	0.95[ASN][1000 genomes]
rs773655	0.85[ASN][1000 genomes]
rs773658	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs773659	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs773660	0.85[ASN][1000 genomes]
rs773661	0.95[ASN][1000 genomes]
rs7962107	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs796475	0.83[EUR][1000 genomes]
rs7967464	0.95[ASN][1000 genomes]
rs7975405	0.95[ASN][1000 genomes]
rs812826	1.00[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7311008	RPS26P10	trans	multi-tissue	Pritchard
rs7311008	LOC441377	trans	multi-tissue	Pritchard
rs7311008	RPS26	cis	multi-tissue	Pritchard
rs7311008	RPS26	cis	lymphoblastoid	seeQTL
rs7311008	LOC644934	trans	multi-tissue	Pritchard
rs7311008	RDH5	cis	lymphoblastoid	seeQTL
rs7311008	LOC441502	trans	multi-tissue	Pritchard
rs7311008	CCDC4	trans	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56554000-56582000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:56554200-56581400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:56554600-56568600	Strong transcription	Ovary	ovary
4	chr12:56555000-56569600	Strong transcription	Brain Substantia Nigra	brain
5	chr12:56555000-56575600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr12:56555000-56579800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:56555000-56580800	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr12:56555000-56580800	Strong transcription	Brain Anterior Caudate	brain
9	chr12:56555000-56581000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:56555200-56573600	Strong transcription	Fetal Lung	lung
11	chr12:56555200-56578800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:56555200-56580600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:56555200-56580800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:56555400-56568600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr12:56555400-56568600	Strong transcription	Esophagus	oesophagus
16	chr12:56555400-56568600	Strong transcription	Gastric	stomach
17	chr12:56555400-56579000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:56555400-56580000	Strong transcription	Placenta	Placenta
19	chr12:56555400-56580600	Strong transcription	Thymus	Thymus
20	chr12:56555400-56580800	Strong transcription	Primary B cells from peripheral blood	blood
21	chr12:56555400-56580800	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr12:56555400-56580800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:56555600-56566600	Strong transcription	Spleen	Spleen
24	chr12:56555600-56569000	Strong transcription	Left Ventricle	heart
25	chr12:56555600-56573600	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr12:56555600-56575400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr12:56555600-56576000	Strong transcription	Brain Cingulate Gyrus	brain
28	chr12:56555600-56580600	Strong transcription	Fetal Brain Female	brain
29	chr12:56555600-56580800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:56555600-56580800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:56555600-56580800	Strong transcription	Liver	Liver
32	chr12:56555600-56580800	Strong transcription	Osteobl	bone
33	chr12:56555800-56568800	Strong transcription	Brain Angular Gyrus	brain
34	chr12:56555800-56569600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:56555800-56573400	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr12:56555800-56580200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr12:56555800-56580600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:56555800-56580600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr12:56555800-56580800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:56555800-56580800	Strong transcription	Fetal Thymus	thymus
41	chr12:56555800-56580800	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:56555800-56581000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:56556000-56568000	Strong transcription	Pancreas	Pancrea
44	chr12:56556000-56573400	Strong transcription	GM12878-XiMat	blood
45	chr12:56556000-56573400	Strong transcription	NHEK	skin
46	chr12:56556000-56573600	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr12:56556000-56578000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:56556000-56580800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:56556000-56580800	Strong transcription	Fetal Intestine Large	intestine
50	chr12:56556000-56581000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links