Variant report

Variant	rs10519788
Chromosome Location	chr15:33382284-33382285
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:33374615..33377190-chr15:33380884..33382943,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1026752	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519781	0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10775202	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10851823	0.92[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11072170	0.84[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11072175	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11072187	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11636433	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11639303	0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12439012	0.92[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12440002	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17235533	0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17235547	0.92[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17816711	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2219159	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2291064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291065	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291066	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2306278	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28510826	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28551066	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28576977	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28603193	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28718544	0.96[ASN][1000 genomes]
rs345794	0.93[ASN][1000 genomes]
rs4779604	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4779605	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4779606	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4780074	0.92[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8033302	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8039005	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs922510	0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs922511	0.83[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10519788	OCA2	cis	cerebellum	SCAN
rs10519788	FAN1	cis	parietal	SCAN
rs10519788	FMN1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33372600-33384200	Weak transcription	Brain Angular Gyrus	brain
2	chr15:33376200-33382600	Weak transcription	Esophagus	oesophagus
3	chr15:33376800-33384600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:33376800-33384600	Weak transcription	NH-A	brain
5	chr15:33377200-33384200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:33379200-33382800	Weak transcription	Fetal Kidney	kidney
7	chr15:33379400-33383200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr15:33379400-33384200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr15:33379400-33386200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:33379600-33382400	Weak transcription	Fetal Thymus	thymus
11	chr15:33380600-33382400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:33380600-33383000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr15:33380600-33387200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:33380800-33382400	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr15:33381000-33382400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:33381000-33382600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr15:33381000-33382800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:33381000-33383000	Enhancers	Stomach Smooth Muscle	stomach
19	chr15:33381000-33383600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr15:33381000-33384800	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr15:33381200-33383000	Enhancers	Hela-S3	cervix
22	chr15:33381200-33383200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:33381400-33382600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr15:33381400-33382600	Enhancers	HSMMtube	muscle
25	chr15:33381400-33383000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr15:33381400-33383000	Enhancers	Fetal Stomach	stomach
27	chr15:33381400-33383000	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr15:33381400-33383000	Enhancers	NHDF-Ad	bronchial
29	chr15:33381400-33383200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:33381400-33383800	Enhancers	Colonic Mucosa	Colon
31	chr15:33381400-33386800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr15:33381400-33387200	Enhancers	Osteobl	bone
33	chr15:33381600-33382600	Enhancers	Fetal Lung	lung
34	chr15:33381600-33382600	Weak transcription	Fetal Muscle Leg	muscle
35	chr15:33381600-33382800	Weak transcription	Psoas Muscle	Psoas
36	chr15:33381600-33383000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr15:33381800-33382600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr15:33381800-33382800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr15:33381800-33383000	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr15:33381800-33383200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr15:33381800-33387200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:33382000-33382400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr15:33382000-33382600	Enhancers	Duodenum Mucosa	Duodenum
44	chr15:33382000-33382600	Enhancers	NHEK	skin
45	chr15:33382000-33383000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:33382000-33383000	Enhancers	HMEC	breast
47	chr15:33382000-33383000	Enhancers	HSMM	muscle
48	chr15:33382000-33383200	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr15:33382200-33382400	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr15:33382200-33382600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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