Variant report

Variant	rs12911676
Chromosome Location	chr15:59646991-59646992
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10851653	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11071432	0.90[ASN][1000 genomes]
rs11071433	0.89[ASN][1000 genomes]
rs11630796	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11631146	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11631451	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11632346	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11635849	0.90[ASN][1000 genomes]
rs11637840	0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11639217	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11854356	0.84[ASN][1000 genomes]
rs11854697	0.84[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11855765	0.93[ASN][1000 genomes]
rs11858264	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11858313	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12050546	0.93[ASN][1000 genomes]
rs12441388	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12442217	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12593355	0.97[ASN][1000 genomes]
rs12899138	0.90[ASN][1000 genomes]
rs12902525	0.80[AMR][1000 genomes]
rs12905793	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1580426	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16941369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17236585	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17302351	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2170895	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28363891	0.94[ASN][1000 genomes]
rs28380572	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28572451	0.95[ASN][1000 genomes]
rs4774327	0.93[ASN][1000 genomes]
rs4775158	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs59107240	0.94[ASN][1000 genomes]
rs61692274	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62012550	0.83[ASN][1000 genomes]
rs6494101	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6494102	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6494105	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs66595425	0.98[ASN][1000 genomes]
rs66991143	0.94[ASN][1000 genomes]
rs67498027	0.93[ASN][1000 genomes]
rs7162228	0.97[ASN][1000 genomes]
rs7168074	0.98[ASN][1000 genomes]
rs7173362	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7178041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8024396	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024879	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024906	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025242	0.97[ASN][1000 genomes]
rs8025360	0.99[ASN][1000 genomes]
rs8031423	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8039327	0.93[ASN][1000 genomes]
rs8041804	0.89[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs965929	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv934082	chr15:59608605-59733211	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv457175	chr15:59609753-59681214	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv569603	chr15:59609753-59681214	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv471246	chr15:59610743-59681214	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv904274	chr15:59623576-59689378	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12911676	BNIP2	cis	cerebellum	SCAN
rs12911676	WDR72	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59623200-59662800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:59624600-59650000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr15:59634800-59662600	Weak transcription	Colonic Mucosa	Colon
4	chr15:59636400-59652800	Weak transcription	HepG2	liver
5	chr15:59637800-59662000	Weak transcription	Right Ventricle	heart
6	chr15:59638600-59653000	Weak transcription	Esophagus	oesophagus
7	chr15:59638600-59654600	Weak transcription	Liver	Liver
8	chr15:59640200-59648000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr15:59641400-59649000	Enhancers	Primary B cells from peripheral blood	blood
10	chr15:59642600-59659400	Weak transcription	Ovary	ovary
11	chr15:59642800-59651600	Weak transcription	Pancreas	Pancrea
12	chr15:59642800-59653200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:59642800-59658600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:59643000-59653000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:59643000-59653000	Weak transcription	HSMMtube	muscle
16	chr15:59643000-59653200	Weak transcription	NHLF	lung
17	chr15:59643000-59656200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:59643000-59659400	Weak transcription	Fetal Intestine Small	intestine
19	chr15:59643200-59648000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:59643200-59650000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:59643200-59650000	Weak transcription	HSMM	muscle
22	chr15:59643600-59648000	Enhancers	Primary B cells from cord blood	blood
23	chr15:59643600-59658800	Weak transcription	Fetal Intestine Large	intestine
24	chr15:59644000-59648000	Enhancers	Primary hematopoietic stem cells	blood
25	chr15:59644000-59653000	Weak transcription	NHDF-Ad	bronchial
26	chr15:59644400-59653000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:59644600-59649800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr15:59644800-59647400	Weak transcription	Brain Anterior Caudate	brain
29	chr15:59644800-59648000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:59644800-59654400	Weak transcription	Osteobl	bone
31	chr15:59644800-59659400	Weak transcription	Right Atrium	heart
32	chr15:59645000-59649000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:59645000-59652800	Weak transcription	Brain Angular Gyrus	brain
34	chr15:59645200-59647400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr15:59645200-59649400	Weak transcription	Colon Smooth Muscle	Colon
36	chr15:59645200-59649600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:59645200-59649800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:59645200-59656400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr15:59645200-59659200	Weak transcription	Fetal Heart	heart
40	chr15:59645200-59662000	Weak transcription	Psoas Muscle	Psoas
41	chr15:59645400-59647600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr15:59645400-59648200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:59645400-59659200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr15:59645400-59659400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:59645600-59647600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr15:59645800-59647600	Enhancers	Primary T cells fromperipheralblood	blood
47	chr15:59646000-59647200	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr15:59646000-59647600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr15:59646000-59647600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr15:59646000-59647800	Enhancers	HMEC	breast

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