Variant report

Variant	rs2564593
Chromosome Location	chr12:30461116-30461117
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXM1	chr12:30460799-30461724	ECC-1	luminal epithelium:	n/a	n/a
2	CEBPB	chr12:30461079-30461749	ECC-1	luminal epithelium:	n/a	n/a
3	FOXM1	chr12:30460770-30461888	ECC-1	luminal epithelium:	n/a	n/a
4	EP300	chr12:30460972-30461797	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr12:30461011-30461934	ECC-1	luminal epithelium:	n/a	n/a
6	TCF12	chr12:30460853-30462003	ECC-1	luminal epithelium:	n/a	n/a
7	ESR1	chr12:30460979-30461735	ECC-1	luminal epithelium:	n/a	n/a
8	EP300	chr12:30460764-30461936	ECC-1	luminal epithelium:	n/a	n/a
9	TCF12	chr12:30460935-30461761	ECC-1	luminal epithelium:	n/a	n/a
10	TEAD4	chr12:30460927-30461752	ECC-1	luminal epithelium:	n/a	n/a
11	ESR1	chr12:30461076-30461718	ECC-1	luminal epithelium:	n/a	n/a
12	USF1	chr12:30461013-30461616	ECC-1	luminal epithelium:	n/a	n/a
13	TEAD4	chr12:30460968-30461801	ECC-1	luminal epithelium:	n/a	n/a
14	NFIC	chr12:30460884-30461881	ECC-1	luminal epithelium:	n/a	n/a
15	ESR1	chr12:30461000-30461677	ECC-1	luminal epithelium:	n/a	n/a
16	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: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10771699	0.95[EUR][1000 genomes]
rs10771700	0.95[EUR][1000 genomes]
rs1262338	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1320923	0.91[JPT][hapmap];0.91[YRI][hapmap];0.83[ASN][1000 genomes]
rs1429626	0.82[EUR][1000 genomes]
rs1429636	0.83[ASN][1000 genomes]
rs1612581	0.85[JPT][hapmap];0.91[YRI][hapmap];0.83[ASN][1000 genomes]
rs1612791	0.83[ASN][1000 genomes]
rs1612949	0.83[ASN][1000 genomes]
rs1613702	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];1.00[ASN][1000 genomes]
rs1652184	0.91[YRI][hapmap]
rs1652185	0.80[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1652186	0.90[JPT][hapmap];0.85[YRI][hapmap];0.83[ASN][1000 genomes]
rs1652187	0.80[ASN][1000 genomes]
rs1652188	0.83[ASN][1000 genomes]
rs1652189	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1652191	0.83[ASN][1000 genomes]
rs1652193	0.83[ASN][1000 genomes]
rs1652195	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1731490	0.91[JPT][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs1731491	0.90[JPT][hapmap];0.91[YRI][hapmap];0.81[ASN][1000 genomes]
rs1731492	0.91[JPT][hapmap];0.91[YRI][hapmap];0.81[ASN][1000 genomes]
rs1731493	0.83[ASN][1000 genomes]
rs1731500	0.83[ASN][1000 genomes]
rs1731503	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1731515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2564526	0.83[ASN][1000 genomes]
rs2564527	0.83[ASN][1000 genomes]
rs2700026	0.83[ASN][1000 genomes]
rs2700028	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2703363	0.83[ASN][1000 genomes]
rs354134	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs354137	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4032080	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4423269	0.91[YRI][hapmap]

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:6 , 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	chr12:30460800-30461200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr12:30461000-30461400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:30461000-30461400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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