Variant report

Variant	rs10876162
Chromosome Location	chr12:51724286-51724287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51715738..51718672-chr12:51724028..51726868,2	MCF-7	breast:
2	chr12:51724277..51726294-chr12:51726344..51728218,2	MCF-7	breast:
3	chr12:51662774..51665391-chr12:51722763..51725080,2	MCF-7	breast:
4	chr12:51686282..51687950-chr12:51722730..51724837,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110934	Chromatin interaction
ENSG00000170545	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10516	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs11169795	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs11169805	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11616158	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12310910	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12582273	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12829179	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830766	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12831721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17860300	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17860301	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17860343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3858624	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3858627	0.84[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs57941347	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61022955	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs68042460	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7133606	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7138439	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7299306	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7299453	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7306746	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7959814	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964134	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9651999	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][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	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv469377	chr12:51690751-51733951	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv558877	chr12:51690751-51733951	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv832408	chr12:51696605-51871339	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10876162	SPATS2	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51718000-51724400	Enhancers	Primary B cells from peripheral blood	blood
2	chr12:51718000-51724400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:51718400-51724400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:51718400-51724400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:51718400-51724400	Enhancers	Placenta	Placenta
6	chr12:51718400-51724400	Enhancers	Fetal Thymus	thymus
7	chr12:51718400-51727800	Weak transcription	Colonic Mucosa	Colon
8	chr12:51720800-51728600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:51720800-51735000	Weak transcription	Esophagus	oesophagus
10	chr12:51721000-51724400	Enhancers	Primary hematopoietic stem cells	blood
11	chr12:51721200-51724600	Weak transcription	A549	lung
12	chr12:51721200-51735000	Weak transcription	NHDF-Ad	bronchial
13	chr12:51721400-51724400	Enhancers	GM12878-XiMat	blood
14	chr12:51722600-51735000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr12:51723200-51724400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr12:51723200-51724400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:51723400-51724400	Enhancers	Osteobl	bone
18	chr12:51723600-51724400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:51723600-51724400	Enhancers	Thymus	Thymus
20	chr12:51723600-51724600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr12:51723600-51725600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:51723800-51724400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:51723800-51724400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:51723800-51724400	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr12:51723800-51724400	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr12:51723800-51724400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:51723800-51724400	Enhancers	HSMMtube	muscle
28	chr12:51723800-51724600	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr12:51723800-51724600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr12:51724000-51724400	Enhancers	Primary T cells from cord blood	blood
31	chr12:51724000-51724400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr12:51724000-51724400	Enhancers	Hela-S3	cervix
33	chr12:51724000-51725000	Enhancers	Primary T cells fromperipheralblood	blood
34	chr12:51724200-51724400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:51724200-51724400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr12:51724200-51724400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:51724200-51724400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:51724200-51724600	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr12:51724200-51724600	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr12:51724200-51724600	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr12:51724200-51726000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr12:51724200-51726200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr12:51724200-51727200	Weak transcription	K562	blood
44	chr12:51724200-51735000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links