Variant report

Variant	rs2802559
Chromosome Location	chr1:224971229-224971230
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	chr1:224968181..224972472-chr1:224972623..224976659,4	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12097622	0.82[EUR][1000 genomes]
rs1316512	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1361923	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1436166	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1436176	0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs1892121	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1898190	0.81[AMR][1000 genomes]
rs1898191	0.81[AMR][1000 genomes]
rs1936632	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2016652	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252950	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2298257	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs2501078	0.82[JPT][hapmap]
rs2574874	0.97[AFR][1000 genomes];1.00[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	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2574879	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2574881	0.81[AMR][1000 genomes]
rs2662906	0.90[ASN][1000 genomes]
rs2662907	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2662922	0.81[AMR][1000 genomes]
rs2662923	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2662924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662925	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662927	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662929	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2802552	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802556	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802558	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802561	0.83[AMR][1000 genomes]
rs2802562	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2802563	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2802740	0.85[AMR][1000 genomes]
rs2802741	0.81[AMR][1000 genomes]
rs2802742	0.81[AMR][1000 genomes]
rs2802744	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2997478	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2997499	0.82[AMR][1000 genomes]
rs2997501	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3012182	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3012184	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs56237431	0.82[EUR][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:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224958000-224972400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:224958800-224972000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:224969800-224971400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:224970000-224973000	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr1:224970200-224971400	Enhancers	Spleen	Spleen
6	chr1:224970200-224971600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:224970400-224971600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:224970400-224971800	Enhancers	Primary hematopoietic stem cells	blood
9	chr1:224970400-224972000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:224970400-224974400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:224970600-224971600	Enhancers	HSMM	muscle
12	chr1:224970600-224971800	Flanking Active TSS	GM12878-XiMat	blood
13	chr1:224971000-224971400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr1:224971000-224971400	Enhancers	Dnd41	blood
15	chr1:224971000-224971800	Enhancers	Primary B cells from peripheral blood	blood
16	chr1:224971000-224971800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:224971000-224972200	Enhancers	Fetal Thymus	thymus
18	chr1:224971000-224975400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:224971000-224975400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:224971200-224971600	Enhancers	Primary T cells from cord blood	blood
21	chr1:224971200-224971800	Enhancers	Thymus	Thymus
22	chr1:224971200-224972200	Weak transcription	HMEC	breast
23	chr1:224971200-224972200	Weak transcription	HSMMtube	muscle

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