Variant report

Variant	rs12747430
Chromosome Location	chr1:86889127-86889128
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	TFAP2C	chr1:86889123-86889949	Hela-S3	cervix:	n/a	n/a
2	FOS	chr1:86888966-86889227	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr1:86889083-86890023	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
CLCA2	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11161808	1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs11161833	0.84[JPT][hapmap]
rs12023726	0.84[ASN][1000 genomes]
rs12023799	0.81[ASN][1000 genomes]
rs12032435	1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs12034967	0.84[ASN][1000 genomes]
rs12037028	0.87[ASN][1000 genomes]
rs12038844	0.87[ASN][1000 genomes]
rs12039899	0.81[ASN][1000 genomes]
rs12042822	0.85[ASN][1000 genomes]
rs12043873	0.87[ASN][1000 genomes]
rs12045012	0.81[ASN][1000 genomes]
rs12046199	0.83[ASN][1000 genomes]
rs12047304	0.84[ASN][1000 genomes]
rs12047913	0.83[ASN][1000 genomes]
rs12048082	0.84[ASN][1000 genomes]
rs12048329	0.84[ASN][1000 genomes]
rs2274999	1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs28688345	0.84[ASN][1000 genomes]
rs28788025	0.84[ASN][1000 genomes]
rs34204564	0.81[ASN][1000 genomes]
rs36096788	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3737671	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[ASN][1000 genomes]
rs3765509	0.81[ASN][1000 genomes]
rs3765984	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3765987	1.00[CEU][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3820038	0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs3820041	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4497186	0.81[ASN][1000 genomes]
rs4656103	0.90[ASN][1000 genomes]
rs55812833	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55825812	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55857117	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56187142	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5744303	1.00[AFR][1000 genomes]
rs5744321	1.00[AFR][1000 genomes]
rs5744349	1.00[AFR][1000 genomes]
rs57955693	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58658794	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59775624	1.00[ASN][1000 genomes]
rs969788	0.84[JPT][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	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86882200-86894800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:86885000-86889200	Enhancers	NHEK	skin
3	chr1:86885200-86889400	Enhancers	HMEC	breast
4	chr1:86885200-86889600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:86887000-86889800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:86887200-86889400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr1:86887200-86889600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:86887200-86889600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:86887200-86895000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:86887400-86889200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:86888000-86890000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:86888000-86890000	Weak transcription	Osteobl	bone
13	chr1:86888000-86890800	Enhancers	Hela-S3	cervix
14	chr1:86888000-86894800	Weak transcription	NHDF-Ad	bronchial
15	chr1:86888200-86890800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:86888200-86894600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:86888400-86889800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:86888600-86889800	Weak transcription	Esophagus	oesophagus
19	chr1:86889000-86889600	Enhancers	Fetal Heart	heart
20	chr1:86889000-86889800	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr1:86889000-86890600	Enhancers	Adipose Nuclei	Adipose

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