Variant report

Variant	rs343144
Chromosome Location	chr2:20601563-20601564
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	MYC	chr2:20601292-20601613	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr2:20601271-20601583	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr2:20601303-20601586	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20592640..20602218-chr2:20644635..20652468,15	MCF-7	breast:

Variant related genes	Relation type
RNA5SP86	TF binding region
ENSG00000143878	Chromatin interaction
ENSG00000228950	Chromatin interaction

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

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

rs_ID	r²[population]
rs10209568	0.90[ASN][1000 genomes]
rs11901184	0.80[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12464277	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1476941	0.93[ASN][1000 genomes]
rs1985318	0.85[ASN][1000 genomes]
rs1985319	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2348705	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs343138	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs343140	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs343142	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs343143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs343147	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs343151	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs343152	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343154	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs343161	0.84[JPT][hapmap]
rs4666306	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4666386	0.93[ASN][1000 genomes]
rs4666387	0.93[ASN][1000 genomes]
rs4666389	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4666390	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62124612	0.83[ASN][1000 genomes]
rs6531236	0.92[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6705947	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6734065	0.82[ASN][1000 genomes]
rs6742129	0.83[LWK][hapmap]
rs67511352	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7563890	0.80[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7564799	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7564810	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7576439	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7576806	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7603518	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7604195	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs953927	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873716	chr2:20572094-20621404	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv581165	chr2:20581058-20616990	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20598000-20601800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr2:20598600-20601600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:20599400-20603400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr2:20599400-20603400	Weak transcription	HSMM	muscle
5	chr2:20600000-20601600	Enhancers	HMEC	breast
6	chr2:20600200-20601800	Enhancers	Stomach Smooth Muscle	stomach
7	chr2:20600200-20602000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:20600600-20601600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:20600600-20602000	Enhancers	NHEK	skin
10	chr2:20600800-20603400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:20601200-20603000	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:20601400-20602600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:20601400-20603000	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:20601400-20614800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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