Variant report

Variant	rs345773
Chromosome Location	chr15:33400054-33400055
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:33359731..33361492-chr15:33397821..33400228,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248905	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11858145	1.00[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs1349964	1.00[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs2604169	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2730050	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs345765	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs345769	0.81[ASN][1000 genomes]
rs345771	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs345772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs345774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs345777	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs345782	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs345787	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs345789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs345790	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs345798	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs345800	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs345801	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4780075	0.85[EUR][1000 genomes]
rs7171647	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv903981	chr15:33207082-33550256	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv568918	chr15:33244672-33446971	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv903982	chr15:33282844-33616150	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv903983	chr15:33388030-33550256	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs345773	OCA2	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33397000-33401200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:33397000-33402400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:33397000-33403000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr15:33397200-33400200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:33397200-33403600	Weak transcription	Fetal Kidney	kidney
6	chr15:33397600-33406000	Weak transcription	NHEK	skin
7	chr15:33397800-33403400	Weak transcription	HSMMtube	muscle
8	chr15:33398200-33400800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr15:33398400-33400200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr15:33398400-33403200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:33398400-33406200	Weak transcription	Fetal Thymus	thymus
12	chr15:33398800-33401400	Enhancers	Osteobl	bone
13	chr15:33399000-33401200	Enhancers	NHDF-Ad	bronchial
14	chr15:33399000-33401400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:33399400-33400200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:33399600-33401000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:33399600-33401200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:33399600-33401200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:33399600-33401200	Enhancers	HSMM	muscle
20	chr15:33399600-33401200	Enhancers	NHLF	lung
21	chr15:33399600-33401400	Enhancers	Muscle Satellite Cultured Cells	--
22	chr15:33399600-33405800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:33399800-33400200	Weak transcription	Placenta	Placenta
24	chr15:33399800-33400600	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr15:33399800-33401200	Enhancers	Hela-S3	cervix
26	chr15:33400000-33400800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:33400000-33400800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links