Variant report

Variant	rs12902525
Chromosome Location	chr15:59619260-59619261
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10851653	0.84[CHB][hapmap]
rs11071428	0.98[ASN][1000 genomes]
rs11071429	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071430	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071431	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631146	0.84[CHB][hapmap]
rs11632346	0.80[AMR][1000 genomes]
rs11637840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs11639217	0.82[AMR][1000 genomes]
rs11854697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs11858264	0.84[CHB][hapmap];0.81[MEX][hapmap]
rs11858313	0.87[CEU][hapmap];0.84[CHB][hapmap]
rs12441388	0.87[CEU][hapmap];0.84[CHB][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs12442217	0.80[AMR][1000 genomes]
rs12593179	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12595769	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905793	0.84[CHB][hapmap];0.81[MEX][hapmap];0.80[AMR][1000 genomes]
rs12911676	0.80[AMR][1000 genomes]
rs1580426	0.80[AMR][1000 genomes]
rs16941337	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941369	0.84[CHB][hapmap]
rs17236578	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17236585	0.87[CEU][hapmap];0.84[CHB][hapmap]
rs17302331	0.81[ASN][1000 genomes]
rs17302351	0.84[CHB][hapmap]
rs2170895	0.80[AMR][1000 genomes]
rs4775158	0.87[CEU][hapmap];0.84[CHB][hapmap]
rs61692274	0.83[EUR][1000 genomes]
rs6494101	0.80[MEX][hapmap];0.82[AMR][1000 genomes]
rs6494102	0.87[CEU][hapmap];0.84[CHB][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes]
rs6494105	0.84[CHB][hapmap]
rs67017396	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67366717	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67552459	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7163650	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164494	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168263	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7170390	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171696	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7177871	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7177984	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178041	0.84[CHB][hapmap];0.81[MEX][hapmap]
rs73426976	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8033217	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033386	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv1794268	chr15:59614874-59637355	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12902525	WDR72	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59600000-59627400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:59606600-59621200	Weak transcription	Fetal Kidney	kidney
3	chr15:59606800-59621400	Weak transcription	Gastric	stomach
4	chr15:59606800-59623000	Weak transcription	Lung	lung
5	chr15:59606800-59631600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:59607000-59620200	Weak transcription	Esophagus	oesophagus
7	chr15:59608600-59619400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr15:59608600-59621400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:59608600-59621400	Weak transcription	Ovary	ovary
10	chr15:59608600-59622600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr15:59608600-59623200	Weak transcription	Psoas Muscle	Psoas
12	chr15:59608600-59623400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr15:59608600-59625800	Weak transcription	HMEC	breast
14	chr15:59608800-59621400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr15:59609800-59620200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:59609800-59620400	Weak transcription	HSMM	muscle
17	chr15:59609800-59620800	Weak transcription	NH-A	brain
18	chr15:59609800-59621400	Weak transcription	Pancreas	Pancrea
19	chr15:59610200-59620400	Weak transcription	Osteobl	bone
20	chr15:59610200-59623000	Weak transcription	Left Ventricle	heart
21	chr15:59610200-59627200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr15:59610600-59620400	Weak transcription	Fetal Heart	heart
23	chr15:59610600-59623000	Weak transcription	Aorta	Aorta
24	chr15:59612200-59625800	Weak transcription	HUVEC	blood vessel
25	chr15:59613800-59626000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:59614000-59620400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:59614200-59621600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:59615000-59619800	Weak transcription	HepG2	liver
29	chr15:59615200-59620000	Weak transcription	Fetal Intestine Small	intestine
30	chr15:59616000-59621400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:59616200-59622600	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr15:59616400-59620400	Weak transcription	NHDF-Ad	bronchial
33	chr15:59616400-59622200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr15:59616400-59624600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr15:59616800-59619800	Weak transcription	Brain Hippocampus Middle	brain
36	chr15:59616800-59620200	Weak transcription	NHLF	lung
37	chr15:59617600-59624400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr15:59618000-59619400	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr15:59618000-59620200	Genic enhancers	A549	lung
40	chr15:59618000-59620800	Weak transcription	Fetal Muscle Leg	muscle
41	chr15:59618200-59619400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:59618200-59619400	Weak transcription	NHEK	skin
43	chr15:59618200-59620000	Weak transcription	Brain Substantia Nigra	brain
44	chr15:59618200-59620400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:59618200-59624200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr15:59618200-59626800	Weak transcription	Brain Angular Gyrus	brain
47	chr15:59618400-59619800	Weak transcription	Hela-S3	cervix
48	chr15:59618800-59619800	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr15:59618800-59619800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:59619000-59619400	Enhancers	Stomach Mucosa	stomach

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