Variant report

Variant	rs1731490
Chromosome Location	chr12:30461323-30461324
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr12:30461181-30461698	ECC-1	luminal epithelium:	n/a	n/a
2	FOXM1	chr12:30460799-30461724	ECC-1	luminal epithelium:	n/a	n/a
3	CEBPB	chr12:30461079-30461749	ECC-1	luminal epithelium:	n/a	n/a
4	FOXM1	chr12:30460770-30461888	ECC-1	luminal epithelium:	n/a	n/a
5	EP300	chr12:30460972-30461797	ECC-1	luminal epithelium:	n/a	n/a
6	MAX	chr12:30461011-30461934	ECC-1	luminal epithelium:	n/a	n/a
7	TCF12	chr12:30460853-30462003	ECC-1	luminal epithelium:	n/a	n/a
8	ESR1	chr12:30460979-30461735	ECC-1	luminal epithelium:	n/a	n/a
9	EP300	chr12:30460764-30461936	ECC-1	luminal epithelium:	n/a	n/a
10	TCF12	chr12:30460935-30461761	ECC-1	luminal epithelium:	n/a	n/a
11	RAD21	chr12:30461211-30461868	ECC-1	luminal epithelium:	n/a	n/a
12	TEAD4	chr12:30460927-30461752	ECC-1	luminal epithelium:	n/a	n/a
13	ESR1	chr12:30461076-30461718	ECC-1	luminal epithelium:	n/a	n/a
14	USF1	chr12:30461013-30461616	ECC-1	luminal epithelium:	n/a	n/a
15	TEAD4	chr12:30460968-30461801	ECC-1	luminal epithelium:	n/a	n/a
16	NFIC	chr12:30460884-30461881	ECC-1	luminal epithelium:	n/a	n/a
17	CEBPB	chr12:30461222-30461696	ECC-1	luminal epithelium:	n/a	n/a
18	ESR1	chr12:30461000-30461677	ECC-1	luminal epithelium:	n/a	n/a
19	NFIC	chr12:30460879-30461740	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:30130967..30132688-chr12:30459870..30462012,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNA5SP356	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10082751	0.94[CEU][hapmap]
rs10082827	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs10082936	0.91[EUR][1000 genomes]
rs10083054	1.00[CEU][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes]
rs10506066	0.88[CEU][hapmap]
rs10771701	0.86[EUR][1000 genomes]
rs10771702	0.87[EUR][1000 genomes]
rs10843721	0.88[EUR][1000 genomes]
rs10843722	0.87[EUR][1000 genomes]
rs11050819	1.00[CEU][hapmap];0.80[JPT][hapmap];0.91[EUR][1000 genomes]
rs11050824	0.88[EUR][1000 genomes]
rs11050825	0.88[EUR][1000 genomes]
rs11834249	0.91[EUR][1000 genomes]
rs11835626	0.88[EUR][1000 genomes]
rs12313162	0.91[EUR][1000 genomes]
rs12322792	0.88[EUR][1000 genomes]
rs12322860	0.88[EUR][1000 genomes]
rs12578380	0.88[EUR][1000 genomes]
rs12580598	0.88[EUR][1000 genomes]
rs12580879	0.88[EUR][1000 genomes]
rs1262338	0.81[ASN][1000 genomes]
rs1320922	1.00[CEU][hapmap];0.80[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1320923	0.94[CEU][hapmap];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]
rs1320925	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1429622	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs1429636	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506373	0.88[EUR][1000 genomes]
rs1506374	0.88[EUR][1000 genomes]
rs1506375	0.88[EUR][1000 genomes]
rs1612581	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1612791	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1612949	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1613702	0.90[JPT][hapmap];0.91[YRI][hapmap];0.83[ASN][1000 genomes]
rs1652138	0.81[CEU][hapmap];0.80[JPT][hapmap];0.85[EUR][1000 genomes]
rs1652184	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1652185	0.83[ASN][1000 genomes]
rs1652186	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1652187	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1652188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1652189	0.90[JPT][hapmap];0.84[YRI][hapmap];0.83[ASN][1000 genomes]
rs1652191	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1652193	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16906211	0.87[ASN][1000 genomes]
rs1731491	1.00[CEU][hapmap];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];0.98[ASN][1000 genomes]
rs1731492	1.00[CEU][hapmap];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];0.98[ASN][1000 genomes]
rs1731493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1731500	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1731503	0.83[ASN][1000 genomes]
rs1731515	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs17464127	0.94[CEU][hapmap];0.80[JPT][hapmap];0.85[EUR][1000 genomes]
rs2115689	0.89[EUR][1000 genomes]
rs2115690	0.89[EUR][1000 genomes]
rs2163114	0.89[EUR][1000 genomes]
rs2163115	0.88[EUR][1000 genomes]
rs2564526	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2564527	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2564593	0.91[JPT][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs2700023	0.88[CEU][hapmap]
rs2700026	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700028	0.81[ASN][1000 genomes]
rs2703363	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4032076	0.88[EUR][1000 genomes]
rs4032077	0.89[EUR][1000 genomes]
rs4032078	0.89[EUR][1000 genomes]
rs4032080	0.80[ASN][1000 genomes]
rs4032081	0.90[EUR][1000 genomes]
rs4032082	0.91[EUR][1000 genomes]
rs4032092	0.88[EUR][1000 genomes]
rs4304873	0.88[EUR][1000 genomes]
rs4304874	0.88[EUR][1000 genomes]
rs4423269	0.84[YRI][hapmap]
rs4426203	0.91[EUR][1000 genomes]
rs4444166	0.88[EUR][1000 genomes]
rs4562911	0.85[EUR][1000 genomes]
rs4564417	0.91[EUR][1000 genomes]
rs57783386	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58747169	0.88[EUR][1000 genomes]
rs73287069	0.88[EUR][1000 genomes]
rs7358618	0.88[EUR][1000 genomes]
rs7358619	0.88[EUR][1000 genomes]
rs7358666	0.88[EUR][1000 genomes]
rs7485854	0.84[EUR][1000 genomes]
rs7977589	0.88[EUR][1000 genomes]
rs906114	0.88[EUR][1000 genomes]
rs906115	0.88[EUR][1000 genomes]
rs9804786	0.88[EUR][1000 genomes]
rs9804787	0.88[EUR][1000 genomes]
rs9805027	0.88[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	nsv832360	chr12:30393329-30555693	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv517916	chr12:30454845-30485611	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv8937	chr12:30457162-30462498	Enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30459200-30461600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:30460600-30461400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:30460600-30461800	Enhancers	NHEK	skin
4	chr12:30461000-30461400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:30461000-30461400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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