Variant report

Variant	rs8025242
Chromosome Location	chr15:59641724-59641725
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59641495..59643626-chr15:59648799..59650877,2	MCF-7	breast:
2	chr15:59637008..59639426-chr15:59640704..59642854,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10851653	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11071430	0.90[AMR][1000 genomes]
rs11071432	0.88[ASN][1000 genomes]
rs11071433	0.87[ASN][1000 genomes]
rs11630796	0.92[ASN][1000 genomes]
rs11631146	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11631451	0.88[ASN][1000 genomes]
rs11632346	0.93[ASN][1000 genomes]
rs11635849	0.88[ASN][1000 genomes]
rs11637840	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11639217	0.92[ASN][1000 genomes]
rs11854356	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11854697	0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11855765	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11858264	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11858313	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12050546	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12441388	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12442217	0.96[ASN][1000 genomes]
rs12593355	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12595769	0.90[AMR][1000 genomes]
rs12899138	0.88[ASN][1000 genomes]
rs12905793	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12911676	0.97[ASN][1000 genomes]
rs1580426	0.96[ASN][1000 genomes]
rs16941369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17236578	0.88[AMR][1000 genomes]
rs17236585	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17302351	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2170895	0.97[ASN][1000 genomes]
rs28363891	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28380572	0.97[ASN][1000 genomes]
rs28572451	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4774327	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4775158	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59107240	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61692274	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62012550	0.80[ASN][1000 genomes]
rs6494101	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6494102	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6494105	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs66595425	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66991143	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67017396	0.90[AMR][1000 genomes]
rs67498027	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67552459	0.83[AMR][1000 genomes]
rs7162228	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168074	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7171696	0.86[AMR][1000 genomes]
rs7173362	0.87[ASN][1000 genomes]
rs7178041	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8024396	0.97[ASN][1000 genomes]
rs8024879	0.97[ASN][1000 genomes]
rs8024906	0.97[ASN][1000 genomes]
rs8025360	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8031423	0.89[ASN][1000 genomes]
rs8039327	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8041804	0.89[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs965929	0.96[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8025242	WDR72	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59623200-59662800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:59623400-59643800	Weak transcription	Lung	lung
3	chr15:59624600-59650000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr15:59626400-59642400	Weak transcription	Pancreas	Pancrea
5	chr15:59631800-59641800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr15:59632000-59642200	Weak transcription	Left Ventricle	heart
7	chr15:59632000-59643600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr15:59634400-59641800	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:59634800-59662600	Weak transcription	Colonic Mucosa	Colon
10	chr15:59636400-59652800	Weak transcription	HepG2	liver
11	chr15:59636600-59643600	Weak transcription	Primary B cells from cord blood	blood
12	chr15:59636800-59642000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:59636800-59642200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr15:59636800-59642200	Genic enhancers	Hela-S3	cervix
15	chr15:59636800-59642600	Weak transcription	Fetal Intestine Small	intestine
16	chr15:59637000-59641800	Weak transcription	Placenta	Placenta
17	chr15:59637000-59642400	Weak transcription	Spleen	Spleen
18	chr15:59637800-59645200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:59637800-59662000	Weak transcription	Right Ventricle	heart
20	chr15:59638400-59642000	Weak transcription	Fetal Intestine Large	intestine
21	chr15:59638600-59641800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr15:59638600-59642200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:59638600-59642400	Weak transcription	Fetal Heart	heart
24	chr15:59638600-59644200	Weak transcription	Brain Angular Gyrus	brain
25	chr15:59638600-59653000	Weak transcription	Esophagus	oesophagus
26	chr15:59638600-59654600	Weak transcription	Liver	Liver
27	chr15:59639200-59641800	Weak transcription	Brain Substantia Nigra	brain
28	chr15:59639400-59642000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:59639600-59642000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr15:59639600-59642000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:59639600-59642200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr15:59639800-59642000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:59640000-59645000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:59640200-59642000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr15:59640200-59642200	Enhancers	HMEC	breast
36	chr15:59640200-59648000	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr15:59640400-59641800	Enhancers	GM12878-XiMat	blood
38	chr15:59640400-59643800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr15:59640600-59642200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr15:59640800-59641800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr15:59640800-59641800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr15:59640800-59641800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr15:59640800-59641800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr15:59640800-59642400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr15:59641000-59641800	Weak transcription	Psoas Muscle	Psoas
46	chr15:59641200-59641800	Enhancers	NHLF	lung
47	chr15:59641200-59642400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr15:59641200-59642800	Enhancers	Aorta	Aorta
49	chr15:59641200-59643800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr15:59641200-59644400	Enhancers	Primary monocytes fromperipheralblood	blood

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