Variant report

Variant	rs2802552
Chromosome Location	chr1:224958498-224958499
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224954304..224956374-chr1:224957483..224959129,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225334	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs12097622	0.82[EUR][1000 genomes]
rs12567091	0.87[YRI][hapmap]
rs1316512	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1361923	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1436166	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16858661	0.87[YRI][hapmap]
rs16858758	0.87[YRI][hapmap]
rs16858831	1.00[YRI][hapmap]
rs16858932	0.87[YRI][hapmap]
rs1892121	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1936632	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1961688	0.87[YRI][hapmap]
rs2005073	0.87[YRI][hapmap]
rs2016652	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252950	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2291227	0.87[YRI][hapmap]
rs2298257	0.80[CEU][hapmap];0.87[JPT][hapmap]
rs2501078	0.82[JPT][hapmap]
rs2574874	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2574876	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2574877	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2574879	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2574881	0.82[AMR][1000 genomes]
rs2662906	0.90[ASN][1000 genomes]
rs2662907	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2662922	0.82[AMR][1000 genomes]
rs2662923	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2662924	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662925	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662927	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662929	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2802556	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802558	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802559	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802561	0.85[AMR][1000 genomes]
rs2802562	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2802563	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2802740	0.81[AMR][1000 genomes]
rs2802744	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2997478	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2997499	0.84[AMR][1000 genomes]
rs2997501	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3012182	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3012184	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs56237431	0.82[EUR][1000 genomes]
rs72629698	0.85[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524125	chr1:224902054-225021860	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224953000-224960800	Weak transcription	Pancreas	Pancrea
2	chr1:224956000-224966400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:224957200-224958600	Enhancers	Stomach Smooth Muscle	stomach
4	chr1:224957400-224958600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:224957400-224958800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:224957400-224958800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:224957600-224958800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:224957600-224958800	Enhancers	Ovary	ovary
9	chr1:224957600-224958800	Enhancers	NHLF	lung
10	chr1:224957800-224958600	Enhancers	Fetal Stomach	stomach
11	chr1:224957800-224958800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:224958000-224958800	Enhancers	Colon Smooth Muscle	Colon
13	chr1:224958000-224972400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:224958200-224958600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:224958200-224958800	Enhancers	NHDF-Ad	bronchial

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