Variant report

Variant	rs11630891
Chromosome Location	chr15:40624128-40624129
allele	A/G
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	chr15:40623843-40624298	A549	lung:	n/a	n/a
2	POLR2A	chr15:40623598-40624283	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr15:40622449-40625435	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr15:40621505-40626199	U87	brain:	n/a	n/a
5	POLR2A	chr15:40623865-40624467	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr15:40621503-40626030	U87	brain:	n/a	n/a
7	POLR2A	chr15:40621475-40625419	U87	brain:	n/a	n/a
8	PBX3	chr15:40622218-40625045	SK-N-SH	brain:	n/a	n/a
9	PBX3	chr15:40623594-40624882	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr15:40619330-40624144	IMR90	lung:	n/a	n/a
11	POLR2A	chr15:40621981-40624857	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr15:40622082-40625539	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr15:40623968-40624868	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr15:40622100-40624714	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr15:40621270-40625419	U87	brain:	n/a	n/a
16	POLR2A	chr15:40619023-40625194	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr15:40621769-40625381	ProgFib	skin:	n/a	n/a
18	POLR2A	chr15:40624037-40624294	Gliobla	brain:	n/a	n/a
19	POLR2A	chr15:40621645-40626480	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr15:40623646-40625414	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr15:40621593-40626881	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr15:40621569-40625028	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr15:40624111-40624267	HepG2	liver:	n/a	n/a
24	POLR2A	chr15:40623982-40624332	HCT-116	colon:	n/a	n/a
25	POLR2A	chr15:40623851-40624272	HepG2	liver:	n/a	n/a
26	JUND	chr15:40622289-40624889	SK-N-SH	brain:	n/a	chr15:40622779-40622793 chr15:40622934-40622942

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40616336..40620318-chr15:40620739..40624439,7	MCF-7	breast:

Variant related genes	Relation type
RNA5SP392	TF binding region
ENSG00000259330	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11634644	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17670483	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17670745	1.00[JPT][hapmap]
rs2118959	0.92[EUR][1000 genomes]
rs28602975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55641696	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62017974	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72731500	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72733403	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs934937	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv827305	chr15:40596162-40625922	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11630891	C15orf52	cis	cerebellum	SCAN
rs11630891	GPR176	cis	cerebellum	SCAN
rs11630891	TMEM26	trans	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40617200-40630200	Weak transcription	A549	lung
2	chr15:40617400-40626000	Weak transcription	Liver	Liver
3	chr15:40617400-40626000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:40617400-40626400	Weak transcription	Pancreas	Pancrea
5	chr15:40617400-40627000	Weak transcription	Gastric	stomach
6	chr15:40617800-40625000	Weak transcription	Psoas Muscle	Psoas
7	chr15:40618000-40624200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr15:40618000-40624400	Enhancers	NHDF-Ad	bronchial
9	chr15:40618000-40625800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr15:40618000-40625800	Weak transcription	Dnd41	blood
11	chr15:40618200-40625800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr15:40618200-40626000	Weak transcription	Stomach Mucosa	stomach
13	chr15:40618400-40624200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr15:40618400-40624400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr15:40618400-40624600	Weak transcription	Primary B cells from cord blood	blood
16	chr15:40618400-40625800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr15:40618400-40625800	Weak transcription	Esophagus	oesophagus
18	chr15:40618400-40626800	Weak transcription	Small Intestine	intestine
19	chr15:40618400-40628200	Weak transcription	Brain Germinal Matrix	brain
20	chr15:40619400-40624200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:40619400-40624800	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr15:40619400-40625400	Genic enhancers	Fetal Stomach	stomach
23	chr15:40619400-40627400	Enhancers	Placenta	Placenta
24	chr15:40619600-40630400	Enhancers	Primary hematopoietic stem cells	blood
25	chr15:40619800-40625000	Enhancers	Fetal Muscle Leg	muscle
26	chr15:40620000-40626000	Enhancers	Rectal Smooth Muscle	rectum
27	chr15:40620000-40627800	Enhancers	Left Ventricle	heart
28	chr15:40620400-40628200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:40620800-40624800	Enhancers	Fetal Muscle Trunk	muscle
30	chr15:40620800-40626000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr15:40620800-40629600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:40621000-40625200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr15:40621000-40626000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:40621000-40626000	Enhancers	Colon Smooth Muscle	Colon
35	chr15:40621000-40627000	Enhancers	HSMMtube	muscle
36	chr15:40621000-40630200	Weak transcription	HepG2	liver
37	chr15:40621000-40637600	Enhancers	Fetal Heart	heart
38	chr15:40621200-40625200	Weak transcription	Adipose Nuclei	Adipose
39	chr15:40621200-40625800	Weak transcription	Thymus	Thymus
40	chr15:40621200-40626200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr15:40621200-40626200	Weak transcription	Fetal Brain Female	brain
42	chr15:40621200-40633400	Weak transcription	Fetal Kidney	kidney
43	chr15:40621400-40624400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:40621400-40625200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:40621400-40625800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr15:40621400-40626000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr15:40621400-40626000	Weak transcription	NHEK	skin
48	chr15:40621400-40626400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr15:40621400-40627000	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr15:40621400-40629800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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