Variant report

Variant	rs12905793
Chromosome Location	chr15:59637351-59637352
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10851653	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11071432	0.85[ASN][1000 genomes]
rs11071433	0.84[ASN][1000 genomes]
rs11630796	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11631146	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11631451	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11632346	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11635849	0.85[ASN][1000 genomes]
rs11637840	0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11639217	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11854697	0.84[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11855765	0.87[ASN][1000 genomes]
rs11858264	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11858313	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12050546	0.87[ASN][1000 genomes]
rs12441388	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12442217	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12593355	0.97[ASN][1000 genomes]
rs12899138	0.85[ASN][1000 genomes]
rs12902525	0.80[AMR][1000 genomes]
rs12911676	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1580426	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16941369	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17236585	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17302351	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2170895	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28363891	0.97[ASN][1000 genomes]
rs28380572	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28572451	0.96[ASN][1000 genomes]
rs4774327	0.87[ASN][1000 genomes]
rs4775158	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs59107240	0.98[ASN][1000 genomes]
rs61692274	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6494101	1.00[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6494102	0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6494105	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs66595425	0.93[ASN][1000 genomes]
rs66991143	1.00[ASN][1000 genomes]
rs67498027	0.97[ASN][1000 genomes]
rs7162228	0.97[ASN][1000 genomes]
rs7168074	0.96[ASN][1000 genomes]
rs7173362	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7178041	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8024396	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8024879	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8024906	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8025242	0.97[ASN][1000 genomes]
rs8025360	0.93[ASN][1000 genomes]
rs8031423	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8039327	0.97[ASN][1000 genomes]
rs8041804	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs965929	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][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	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
7	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
rs12905793	WDR72	cis	parietal	SCAN

Chromatin state (count:52 , 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	chr15:59623400-59641200	Weak transcription	Aorta	Aorta
3	chr15:59623400-59643800	Weak transcription	Lung	lung
4	chr15:59624400-59637800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:59624600-59650000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr15:59626400-59641400	Weak transcription	HUVEC	blood vessel
7	chr15:59626400-59642400	Weak transcription	Pancreas	Pancrea
8	chr15:59628000-59637800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr15:59628400-59637800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:59628600-59639200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:59631800-59637600	Weak transcription	Right Ventricle	heart
12	chr15:59631800-59641600	Weak transcription	HSMM	muscle
13	chr15:59631800-59641800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr15:59632000-59637800	Weak transcription	Brain Substantia Nigra	brain
15	chr15:59632000-59641600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:59632000-59641600	Weak transcription	NH-A	brain
17	chr15:59632000-59642200	Weak transcription	Left Ventricle	heart
18	chr15:59632000-59643600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:59632200-59641400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr15:59632400-59639200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:59632600-59637400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:59632600-59637800	Weak transcription	Osteobl	bone
23	chr15:59632600-59638000	Weak transcription	Brain Angular Gyrus	brain
24	chr15:59632600-59639200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:59632600-59641400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:59632800-59637400	Weak transcription	NHDF-Ad	bronchial
27	chr15:59632800-59639400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:59632800-59640200	Weak transcription	HMEC	breast
29	chr15:59633000-59637600	Weak transcription	NHEK	skin
30	chr15:59633000-59641200	Weak transcription	NHLF	lung
31	chr15:59633200-59639400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr15:59634400-59641800	Weak transcription	Brain Hippocampus Middle	brain
33	chr15:59634600-59640800	Genic enhancers	A549	lung
34	chr15:59634800-59662600	Weak transcription	Colonic Mucosa	Colon
35	chr15:59636000-59637400	ZNF genes & repeats	GM12878-XiMat	blood
36	chr15:59636200-59637600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:59636400-59637600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:59636400-59652800	Weak transcription	HepG2	liver
39	chr15:59636600-59638600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr15:59636600-59643600	Weak transcription	Primary B cells from cord blood	blood
41	chr15:59636800-59637800	Weak transcription	Primary B cells from peripheral blood	blood
42	chr15:59636800-59638400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr15:59636800-59640200	Weak transcription	Psoas Muscle	Psoas
44	chr15:59636800-59642000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr15:59636800-59642200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr15:59636800-59642200	Genic enhancers	Hela-S3	cervix
47	chr15:59636800-59642600	Weak transcription	Fetal Intestine Small	intestine
48	chr15:59637000-59641800	Weak transcription	Placenta	Placenta
49	chr15:59637000-59642400	Weak transcription	Spleen	Spleen
50	chr15:59637200-59638600	Enhancers	Liver	Liver

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