Variant report

Variant	rs12616801
Chromosome Location	chr2:113730425-113730426
allele	A/G
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	FOS	chr2:113729921-113730646	MCF10A-Er-Src	breast:	n/a	chr2:113730501-113730511 chr2:113730495-113730507 chr2:113730501-113730511 chr2:113730503-113730514 chr2:113730502-113730510
2	MYC	chr2:113729921-113730627	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr2:113729883-113730489	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr2:113730015-113730450	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr2:113729851-113730726	MCF10A-Er-Src	breast:	n/a	chr2:113730501-113730511 chr2:113730495-113730507 chr2:113730501-113730511 chr2:113730503-113730514 chr2:113730502-113730510
6	STAT3	chr2:113729947-113730713	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr2:113729935-113730782	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr2:113729870-113730644	MCF10A-Er-Src	breast:	n/a	chr2:113730501-113730511 chr2:113730495-113730507 chr2:113730501-113730511 chr2:113730503-113730514 chr2:113730502-113730510
9	MYC	chr2:113729901-113730555	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
IL36G	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10171072	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10184412	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10205381	0.81[YRI][hapmap]
rs11676013	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs11683399	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11690185	0.80[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs11695110	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11696039	0.84[JPT][hapmap]
rs12464758	0.80[AMR][1000 genomes]
rs12465526	0.80[AMR][1000 genomes]
rs12466604	0.80[AMR][1000 genomes]
rs12466653	0.80[AMR][1000 genomes]
rs12466697	0.81[ASN][1000 genomes]
rs12614316	0.80[AMR][1000 genomes]
rs12614988	0.80[AMR][1000 genomes]
rs12618418	0.81[ASN][1000 genomes]
rs12993351	0.80[AMR][1000 genomes]
rs13033104	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1317913	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13418326	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305152	0.96[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35880601	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66591921	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6705432	0.80[AMR][1000 genomes]
rs6722962	0.80[AMR][1000 genomes]
rs6723197	0.80[AMR][1000 genomes]
rs6733001	0.80[AMR][1000 genomes]
rs6733003	0.80[AMR][1000 genomes]
rs67995749	0.80[AMR][1000 genomes]
rs725139	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs725140	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532471	chr2:113682449-113862981	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv2880	chr2:113716802-113736921	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv2753453	chr2:113726882-113730425	Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1007254	chr2:113726982-113887782	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv535894	chr2:113726982-113887782	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 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	chr2:113729200-113731600	Enhancers	HMEC	breast
2	chr2:113729400-113731400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:113729600-113731200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:113729600-113731200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:113730200-113730600	Flanking Active TSS	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links