Variant report

Variant	rs7178041
Chromosome Location	chr15:59661404-59661405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:59660865-59666082	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr15:59660777-59661556	H1-hESC	embryonic stem cell:	n/a	n/a
3	MTA3	chr15:59661392-59662996	GM12878	blood:	n/a	n/a
4	POLR2A	chr15:59660476-59665554	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:59654267..59656518-chr15:59659783..59662532,2	K562	blood:
2	chr15:59658868..59661498-chr15:59663501..59666057,3	MCF-7	breast:
3	chr15:59661077..59662857-chr15:59663760..59666733,2	MCF-7	breast:

Variant related genes	Relation type
FAM81A	TF binding region
ENSG00000157470	Chromatin interaction
ENSG00000157483	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10851653	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.82[YRI][hapmap];0.98[ASN][1000 genomes]
rs11071432	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11071433	0.98[ASN][1000 genomes]
rs11630796	0.84[ASN][1000 genomes]
rs11631146	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11631451	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632346	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11634604	0.88[ASN][1000 genomes]
rs11635849	0.99[ASN][1000 genomes]
rs11637840	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11639217	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11854356	0.94[ASN][1000 genomes]
rs11854697	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11855765	0.97[ASN][1000 genomes]
rs11858264	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11858313	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12050546	0.97[ASN][1000 genomes]
rs12441388	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12442217	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12593355	0.87[ASN][1000 genomes]
rs12899138	0.99[ASN][1000 genomes]
rs12905793	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]
rs12911676	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1580426	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16941369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17236585	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17302351	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2170895	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28363891	0.85[ASN][1000 genomes]
rs28380572	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28572451	0.86[ASN][1000 genomes]
rs4774327	0.97[ASN][1000 genomes]
rs4775158	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs59107240	0.84[ASN][1000 genomes]
rs61692274	0.83[ASN][1000 genomes]
rs62012550	0.91[ASN][1000 genomes]
rs6494101	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6494102	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6494105	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs66595425	0.91[ASN][1000 genomes]
rs66991143	0.84[ASN][1000 genomes]
rs67498027	0.84[ASN][1000 genomes]
rs7162228	0.87[ASN][1000 genomes]
rs7168074	0.88[ASN][1000 genomes]
rs7173362	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024396	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8024879	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8024906	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8025242	0.87[ASN][1000 genomes]
rs8025360	0.89[ASN][1000 genomes]
rs8031423	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8039327	0.84[ASN][1000 genomes]
rs8041804	0.89[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs965929	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv904275	chr15:59648633-59726610	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	n/a
8	nsv904276	chr15:59648633-59743010	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7178041	WDR72	cis	parietal	SCAN
rs7178041	BNIP2	cis	cerebellum	SCAN

Chromatin state (count:87 , 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	chr15:59634800-59662600	Weak transcription	Colonic Mucosa	Colon
3	chr15:59637800-59662000	Weak transcription	Right Ventricle	heart
4	chr15:59645200-59662000	Weak transcription	Psoas Muscle	Psoas
5	chr15:59646600-59662200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr15:59646800-59662600	Weak transcription	Gastric	stomach
7	chr15:59647000-59662400	Weak transcription	Adipose Nuclei	Adipose
8	chr15:59648600-59663200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:59648800-59662200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:59649000-59663400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr15:59650600-59663400	Weak transcription	Fetal Stomach	stomach
12	chr15:59653400-59662000	Weak transcription	Placenta	Placenta
13	chr15:59653400-59662200	Weak transcription	Spleen	Spleen
14	chr15:59653400-59662600	Weak transcription	Left Ventricle	heart
15	chr15:59653400-59663400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:59653600-59662800	Weak transcription	HSMMtube	muscle
17	chr15:59656600-59663000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:59656800-59662200	Weak transcription	Stomach Mucosa	stomach
19	chr15:59657000-59662200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:59657800-59661800	Weak transcription	Primary B cells from cord blood	blood
21	chr15:59658800-59662000	Weak transcription	Fetal Muscle Leg	muscle
22	chr15:59659600-59661800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:59659600-59662800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:59659800-59661600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:59659800-59662000	Weak transcription	Aorta	Aorta
26	chr15:59659800-59662200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:59659800-59662200	Weak transcription	Lung	lung
28	chr15:59659800-59662200	Weak transcription	Pancreas	Pancrea
29	chr15:59659800-59662400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr15:59659800-59662400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr15:59659800-59662600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr15:59659800-59662600	Weak transcription	Fetal Kidney	kidney
33	chr15:59659800-59662600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr15:59659800-59662600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr15:59659800-59662800	Weak transcription	Fetal Intestine Large	intestine
36	chr15:59659800-59663200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr15:59659800-59663400	Weak transcription	Ovary	ovary
38	chr15:59659800-59663400	Weak transcription	Small Intestine	intestine
39	chr15:59660000-59661600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr15:59660000-59661600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr15:59660000-59661600	Weak transcription	NHDF-Ad	bronchial
42	chr15:59660000-59661800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr15:59660000-59661800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr15:59660000-59661800	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr15:59660000-59662000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr15:59660000-59662000	Weak transcription	Brain Angular Gyrus	brain
47	chr15:59660000-59662200	Weak transcription	Liver	Liver
48	chr15:59660000-59662200	Weak transcription	Esophagus	oesophagus
49	chr15:59660000-59662200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr15:59660000-59662200	Weak transcription	Osteobl	bone

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