Variant report

Variant	rs345790
Chromosome Location	chr15:33391179-33391180
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs11858145	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs1349964	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs2604169	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2730050	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs345765	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs345771	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs345772	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs345773	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs345774	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs345777	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs345782	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs345787	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs345789	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs345798	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs345800	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs345801	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4780075	0.86[EUR][1000 genomes]
rs7171647	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8024232	0.81[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
rs345790	OCA2	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33384800-33391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:33384800-33395000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:33384800-33395400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr15:33385000-33396400	Weak transcription	Fetal Kidney	kidney
5	chr15:33388800-33392200	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr15:33389200-33393000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:33389400-33394200	Enhancers	NHDF-Ad	bronchial
8	chr15:33389600-33391200	Enhancers	NH-A	brain
9	chr15:33389600-33391400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr15:33389800-33391800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:33389800-33392400	Enhancers	HSMM	muscle
12	chr15:33389800-33392800	Enhancers	Hela-S3	cervix
13	chr15:33389800-33394200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:33390000-33391200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr15:33390000-33391800	Enhancers	HMEC	breast
16	chr15:33390200-33391600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:33390400-33391200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:33390400-33391200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:33390400-33392200	Enhancers	NHLF	lung
20	chr15:33390400-33392800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:33390400-33392800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:33390600-33391400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:33390800-33391800	Enhancers	NHEK	skin
24	chr15:33390800-33392000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr15:33390800-33392200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:33390800-33392200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:33390800-33392400	Enhancers	Osteobl	bone
28	chr15:33390800-33392600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:33390800-33394200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:33390800-33396200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:33391000-33392000	Enhancers	HSMMtube	muscle
32	chr15:33391000-33396200	Weak transcription	HUVEC	blood vessel
33	chr15:33391000-33396400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:33391000-33396600	Weak transcription	Fetal Muscle Leg	muscle

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