Variant report

Variant	rs4761981
Chromosome Location	chr12:51674501-51674502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51475694..51478685-chr12:51673331..51675539,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10747609	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10783426	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10783427	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs10783428	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10876156	0.82[CEU][hapmap]
rs10876159	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1130641	0.83[CEU][hapmap]
rs1362963	0.94[CEU][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs1877260	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1877261	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1975004	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2271821	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2359449	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3210837	0.94[CEU][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs3886185	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3951438	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4761814	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4761815	1.00[CEU][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4761935	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4761938	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4761966	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4761969	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4761995	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];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4762011	0.80[EUR][1000 genomes]
rs4991750	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6580820	1.00[CEU][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7133314	0.80[CEU][hapmap]
rs7133495	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7135343	0.80[EUR][1000 genomes]
rs7135840	0.80[EUR][1000 genomes]
rs7136290	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7296747	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7304578	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7306505	0.80[EUR][1000 genomes]
rs7311434	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7316347	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7316569	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7957667	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9325148	0.83[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]

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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4761981	LOC57228	cis	multi-tissue	Pritchard
rs4761981	COL2A1	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51664600-51683200	Weak transcription	Spleen	Spleen
2	chr12:51664600-51692800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:51664800-51685800	Weak transcription	Esophagus	oesophagus
4	chr12:51665000-51674600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:51665200-51674800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:51665400-51674600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr12:51665400-51674800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr12:51665400-51675000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:51665400-51679800	Weak transcription	Liver	Liver
10	chr12:51665600-51678200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:51669200-51674600	Weak transcription	A549	lung
12	chr12:51669400-51678200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:51669600-51674600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr12:51671000-51674600	Weak transcription	Primary T cells from cord blood	blood
15	chr12:51673000-51676000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr12:51673200-51685200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:51673400-51675000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr12:51673400-51675200	Weak transcription	Osteobl	bone
19	chr12:51673400-51684800	Weak transcription	GM12878-XiMat	blood
20	chr12:51673600-51675000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:51673800-51679400	Strong transcription	Thymus	Thymus
22	chr12:51673800-51685400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr12:51673800-51697600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:51674000-51674800	Weak transcription	Primary B cells from cord blood	blood
25	chr12:51674000-51675800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:51674000-51680600	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr12:51674000-51683400	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:51674000-51698400	Strong transcription	Fetal Thymus	thymus
29	chr12:51674000-51701400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:51674200-51685400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr12:51674200-51685600	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr12:51674200-51704000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr12:51674400-51675000	Enhancers	NHEK	skin
34	chr12:51674400-51675800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:51674400-51676000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr12:51674400-51676200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:51674400-51679000	Strong transcription	Primary B cells from peripheral blood	blood
38	chr12:51674400-51685200	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr12:51674400-51698400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr12:51674400-51698600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:51674400-51698800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:51674400-51700600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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