Variant report

Variant	rs16949914
Chromosome Location	chr12:120493891-120493892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr12:120493020-120493913	Hela-S3	cervix:	n/a	chr12:120493667-120493678
2	STAT3	chr12:120492967-120493903	MCF10A-Er-Src	breast:	n/a	n/a
3	EP300	chr12:120493409-120493894	HepG2	liver:	n/a	n/a
4	RFX5	chr12:120493128-120493902	Hela-S3	cervix:	n/a	n/a
5	STAT3	chr12:120493149-120493920	Hela-S3	cervix:	n/a	n/a
6	FOS	chr12:120492952-120493902	MCF10A-Er-Src	breast:	n/a	chr12:120493355-120493364 chr12:120493224-120493236
7	MYC	chr12:120492969-120493904	MCF10A-Er-Src	breast:	n/a	n/a
8	TCF12	chr12:120493023-120493944	A549	lung:	n/a	n/a
9	SMARCC1	chr12:120493038-120494082	Hela-S3	cervix:	n/a	n/a
10	CEBPB	chr12:120493362-120493939	A549	lung:	n/a	chr12:120493667-120493678
11	POLR2A	chr12:120492887-120494028	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr12:120492965-120493895	MCF10A-Er-Src	breast:	n/a	chr12:120493355-120493364 chr12:120493224-120493236

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:120484758..120487182-chr12:120493817..120495505,2	MCF-7	breast:
2	chr12:120425499..120429715-chr12:120491495..120494427,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255575	TF binding region
ENSG00000272464	Chromatin interaction
ENSG00000135127	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1054631	1.00[ASN][1000 genomes]
rs16949854	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16949862	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16949870	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286041	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28613380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56105460	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56152568	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56939014	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57155388	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57339959	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57458743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59868595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59911114	0.93[EUR][1000 genomes]
rs60106911	1.00[ASN][1000 genomes]
rs60223336	1.00[ASN][1000 genomes]
rs60590470	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60742518	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61514727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490279	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6490282	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132099	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7139151	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7297564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298081	1.00[CHB][hapmap];1.00[JPT][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]
rs7304560	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956221	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957325	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899554	chr12:120389613-120513625	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120480000-120499200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr12:120480000-120499200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr12:120486400-120498600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:120486600-120498600	Weak transcription	Gastric	stomach
5	chr12:120486600-120499200	Weak transcription	Thymus	Thymus
6	chr12:120486800-120512000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr12:120487000-120499400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr12:120487000-120502400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr12:120487000-120502400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:120487200-120499400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr12:120487200-120499800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr12:120487400-120498200	Weak transcription	Primary T cells from cord blood	blood
13	chr12:120487800-120512200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr12:120488000-120498000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr12:120492000-120495000	Enhancers	Hela-S3	cervix
16	chr12:120492800-120494800	Enhancers	Liver	Liver
17	chr12:120493000-120494800	Enhancers	HepG2	liver
18	chr12:120493000-120503200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:120493200-120494000	Enhancers	NHEK	skin
20	chr12:120493600-120495000	Enhancers	HMEC	breast
21	chr12:120493800-120497800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:120493800-120501600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:120493800-120523800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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