Variant report

Variant	rs3852257
Chromosome Location	chr7:18871692-18871693
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	FOS	chr7:18871684-18871919	MCF10A-Er-Src	breast:	n/a	chr7:18871814-18871822 chr7:18871814-18871821 chr7:18871814-18871822
2	ESR1	chr7:18871559-18871923	ECC-1	luminal epithelium:	n/a	n/a
3	GATA3	chr7:18871543-18871808	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
HDAC9	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12540774	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12699994	0.84[CHB][hapmap];0.81[EUR][1000 genomes]
rs13233322	0.80[CHB][hapmap]
rs13238389	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17349860	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2016515	0.90[CEU][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2073964	0.80[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3852256	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6461385	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6461387	0.84[CHB][hapmap]
rs6951522	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7795433	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs957958	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs957960	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498112	chr7:18677922-18991946	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv887813	chr7:18720135-18995552	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv887814	chr7:18751998-18886177	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 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	chr7:18854000-18874400	Weak transcription	Aorta	Aorta
2	chr7:18866800-18885200	Weak transcription	Primary B cells from cord blood	blood
3	chr7:18867200-18882400	Weak transcription	Left Ventricle	heart
4	chr7:18868200-18879400	Weak transcription	HSMMtube	muscle
5	chr7:18868800-18887400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:18869600-18874400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:18869800-18874200	Weak transcription	Fetal Lung	lung
8	chr7:18870000-18874200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr7:18870000-18874400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:18870000-18874400	Weak transcription	Fetal Stomach	stomach
11	chr7:18870000-18874600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:18870000-18874600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:18870600-18874200	Weak transcription	Fetal Kidney	kidney
14	chr7:18871000-18872000	Enhancers	NHDF-Ad	bronchial
15	chr7:18871200-18872000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:18871400-18871800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:18871400-18871800	Enhancers	HMEC	breast
18	chr7:18871600-18872000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:18871600-18872000	Enhancers	Adipose Nuclei	Adipose
20	chr7:18871600-18874400	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links