Variant report

Variant	rs921286
Chromosome Location	chr12:122227691-122227692
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122222027..122223531-chr12:122224930..122227928,2	MCF-7	breast:
2	chr12:122219448..122221422-chr12:122224935..122227842,2	MCF-7	breast:
3	chr12:122134034..122138136-chr12:122226162..122228726,3	MCF-7	breast:
4	chr12:122188669..122193873-chr12:122227176..122233304,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188735	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1004390	0.90[EUR][1000 genomes]
rs11043202	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043207	1.00[CEU][hapmap]
rs1168663	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1168664	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168665	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1168666	1.00[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs1168668	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168669	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168671	1.00[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168672	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168673	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12307227	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313997	0.89[ASN][1000 genomes]
rs12314801	0.89[ASN][1000 genomes]
rs12820413	0.82[ASN][1000 genomes]
rs12823194	0.84[EUR][1000 genomes]
rs1667578	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1667579	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1795965	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795966	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2019561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019562	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2122266	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2707057	0.82[ASN][1000 genomes]
rs2707066	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2707067	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712852	1.00[CEU][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7957564	0.90[EUR][1000 genomes]
rs7974348	1.00[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs895951	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895952	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs895954	1.00[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs895957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs930665	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv899566	chr12:122167095-122265106	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv899567	chr12:122203680-122281575	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv984477	chr12:122226309-122271532	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs921286	LOC338799	cis	parietal	SCAN
rs921286	LOC338799	cis	multi-tissue	Pritchard
rs921286	MPHOSPH9	cis	cerebellum	SCAN
rs921286	CCDC60	cis	parietal	SCAN
rs921286	AC084018.1	cis	Skin Sun Exposed Lower leg	GTEx
rs921286	LOC338799	cis	cerebellum	SCAN
rs921286	SBNO1	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122206400-122228200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr12:122206400-122230600	Weak transcription	Brain Angular Gyrus	brain
3	chr12:122211600-122231200	Weak transcription	Brain Hippocampus Middle	brain
4	chr12:122211800-122231600	Weak transcription	Brain Substantia Nigra	brain
5	chr12:122214200-122228200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:122217800-122230400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr12:122219000-122229800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:122219200-122230600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:122219200-122230600	Weak transcription	Fetal Brain Female	brain
10	chr12:122219600-122230800	Weak transcription	Brain Germinal Matrix	brain
11	chr12:122220400-122230400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:122220400-122230600	Weak transcription	Brain Anterior Caudate	brain
13	chr12:122220600-122228000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:122220600-122230400	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:122220600-122230400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr12:122220800-122228000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:122220800-122228200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:122220800-122229600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:122221200-122230600	Weak transcription	Right Atrium	heart
20	chr12:122223200-122228000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:122223200-122231400	Weak transcription	HSMM	muscle
22	chr12:122223600-122228600	Enhancers	Placenta	Placenta
23	chr12:122224000-122229400	Genic enhancers	Fetal Intestine Small	intestine
24	chr12:122224200-122228400	Enhancers	Stomach Mucosa	stomach
25	chr12:122224200-122228800	Genic enhancers	Fetal Intestine Large	intestine
26	chr12:122224200-122229000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr12:122224400-122227800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr12:122224600-122231200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:122224800-122231000	Weak transcription	Osteobl	bone
30	chr12:122225200-122229400	Weak transcription	HMEC	breast
31	chr12:122225200-122229600	Weak transcription	NHEK	skin
32	chr12:122225200-122231400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr12:122225400-122227800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:122225400-122228000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:122225400-122228200	Weak transcription	Gastric	stomach
36	chr12:122225400-122229600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:122225400-122229600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:122225400-122230000	Enhancers	Spleen	Spleen
39	chr12:122225400-122231000	Weak transcription	Pancreas	Pancrea
40	chr12:122225600-122230400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:122225800-122228800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr12:122225800-122233200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr12:122226000-122228800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr12:122226000-122228800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:122226000-122228800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr12:122226000-122228800	Flanking Active TSS	GM12878-XiMat	blood
47	chr12:122226000-122229600	Transcr. at gene 5' and 3'	Hela-S3	cervix
48	chr12:122226200-122227800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:122226200-122228400	Genic enhancers	HepG2	liver
50	chr12:122226200-122228800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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