Variant report

Variant	rs883200
Chromosome Location	chr1:86888498-86888499
allele	C/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	STAT3	chr1:86888366-86888683	MCF10A-Er-Src	breast:	n/a	chr1:86888494-86888505 chr1:86888601-86888613
2	FOS	chr1:86888301-86888593	MCF10A-Er-Src	breast:	n/a	chr1:86888510-86888519
3	STAT3	chr1:86888391-86888623	MCF10A-Er-Src	breast:	n/a	chr1:86888494-86888505 chr1:86888601-86888613
4	STAT3	chr1:86888272-86888656	MCF10A-Er-Src	breast:	n/a	chr1:86888494-86888505 chr1:86888601-86888613

Variant related genes	Relation type
CLCA2	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10493789	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10747328	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10873777	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10873782	0.98[AFR][1000 genomes]
rs11161820	0.85[ASN][1000 genomes]
rs1158505	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1158506	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1182102	0.80[EUR][1000 genomes]
rs1334143	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1334144	0.98[AFR][1000 genomes]
rs1334146	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1334147	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1334148	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1334150	0.84[ASN][1000 genomes]
rs166626	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs166627	0.86[ASN][1000 genomes]
rs175363	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs187971	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1931363	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2104962	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2104963	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2151708	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2151709	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2250857	0.86[ASN][1000 genomes]
rs272491	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs272492	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs272494	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs272498	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs272504	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs272507	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs272510	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs272511	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs272516	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3765975	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3765978	0.85[ASN][1000 genomes]
rs405424	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4288573	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4292929	0.85[ASN][1000 genomes]
rs6695671	0.85[EUR][1000 genomes];0.91[ASN][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	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:20 , 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	chr1:86887800-86888600	Enhancers	Esophagus	oesophagus
12	chr1:86888000-86889000	Weak transcription	Fetal Heart	heart
13	chr1:86888000-86890000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:86888000-86890000	Weak transcription	Osteobl	bone
15	chr1:86888000-86890800	Enhancers	Hela-S3	cervix
16	chr1:86888000-86894800	Weak transcription	NHDF-Ad	bronchial
17	chr1:86888200-86890800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr1:86888200-86894600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:86888400-86889000	Weak transcription	Adipose Nuclei	Adipose
20	chr1:86888400-86889800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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