Variant report

Variant	rs12570425
Chromosome Location	chr10:213748-213749
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:180810..183645-chr10:213467..216539,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000015171	Chromatin interaction

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

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

rs_ID	r²[population]
rs1017361	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs11251203	0.94[EUR][1000 genomes]
rs1367896	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1476129	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs1545003	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2007293	0.94[EUR][1000 genomes]
rs2043201	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2303990	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2436024	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2436025	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2436028	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2436031	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs2448365	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2448369	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2448374	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2448376	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2448377	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2448379	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2448382	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2496274	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2496277	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2496279	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs3001994	0.94[EUR][1000 genomes]
rs3123252	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs3132006	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs3740303	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4390277	0.82[EUR][1000 genomes]
rs4582897	0.83[ASN][1000 genomes]
rs4593933	0.94[EUR][1000 genomes]
rs4600135	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs4880517	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6560742	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7478542	0.94[EUR][1000 genomes]
rs7905732	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs7914050	0.94[EUR][1000 genomes]
rs9329277	0.82[EUR][1000 genomes]
rs9329281	0.94[EUR][1000 genomes]
rs9419433	0.94[EUR][1000 genomes]
rs9419436	0.94[EUR][1000 genomes]
rs9419475	1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs9419499	0.94[EUR][1000 genomes]
rs9419562	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531919	chr10:60001-668649	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1040332	chr10:72797-244561	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1044775	chr10:72797-250662	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1047868	chr10:72797-259003	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1048232	chr10:72797-274675	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr10:190400-215200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr10:194200-228200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr10:196800-215000	Weak transcription	Fetal Intestine Large	intestine
4	chr10:197800-219800	Weak transcription	HUVEC	blood vessel
5	chr10:200000-228000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr10:200400-226800	Weak transcription	HSMM	muscle
7	chr10:200400-230400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr10:201000-214600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr10:207200-226800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr10:208000-214800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr10:208200-293000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr10:209800-215800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr10:209800-225800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr10:209800-226600	Weak transcription	Liver	Liver
15	chr10:210600-219200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr10:210800-224800	Weak transcription	Ovary	ovary
17	chr10:211800-214800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr10:212800-226400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr10:213000-214800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr10:213200-215000	Weak transcription	Adipose Nuclei	Adipose

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