Variant report

Variant	rs10239759
Chromosome Location	chr7:149542524-149542525
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	MAFK	chr7:149542365-149542649	HepG2	liver:	n/a	chr7:149542537-149542548 chr7:149542536-149542550 chr7:149542538-149542549 chr7:149542537-149542548 chr7:149542538-149542549
2	POLR2A	chr7:149542004-149544462	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr7:149542278-149542620	HepG2	liver:	n/a	chr7:149542418-149542429
4	ZKSCAN1	chr7:149542451-149542527	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:149541998..149544901-chr7:149565491..149567643,2	MCF-7	breast:
2	chr7:149541182..149543839-chr7:149558694..149561478,2	MCF-7	breast:
3	chr7:149534234..149537343-chr7:149542425..149544829,4	MCF-7	breast:
4	chr7:149542392..149544119-chr7:149568083..149570783,2	K562	blood:

Variant related genes	Relation type
ZNF862	TF binding region
ENSG00000106479	Chromatin interaction
ENSG00000171130	Chromatin interaction
ENSG00000273419	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12530607	0.91[CEU][hapmap]
rs12534509	1.00[CEU][hapmap]
rs28715524	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3735326	0.83[TSI][hapmap]
rs62621204	0.97[ASN][1000 genomes]
rs6972739	0.90[ASN][1000 genomes]
rs7809988	0.92[CHB][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034350	chr7:149264094-149666356	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv539190	chr7:149264094-149666356	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023901	chr7:149364044-149747442	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv539191	chr7:149364044-149747442	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv469576	chr7:149379626-149563233	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1031581	chr7:149386249-149570178	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv539192	chr7:149386249-149570178	Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv831184	chr7:149424835-149600093	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	esv2758139	chr7:149441590-149956415	Strong transcription Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	esv2759571	chr7:149441590-149956415	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	nsv521861	chr7:149458623-149582906	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
12	nsv889409	chr7:149458623-149585379	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv1029471	chr7:149496177-149810381	Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
14	nsv539193	chr7:149496177-149810381	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
15	nsv1033095	chr7:149508083-149781872	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
16	nsv608987	chr7:149509981-149547703	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	nsv1029484	chr7:149539914-149599326	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10239759	TMEM176B	cis	parietal	SCAN
rs10239759	C7orf33	cis	cerebellum	SCAN
rs10239759	ACTR3C	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:149536400-149542600	Weak transcription	Aorta	Aorta
2	chr7:149536400-149543000	Weak transcription	Ovary	ovary
3	chr7:149536400-149543400	Weak transcription	Placenta	Placenta
4	chr7:149536400-149543800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr7:149536400-149544800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr7:149536400-149544800	Weak transcription	Spleen	Spleen
7	chr7:149536400-149547000	Weak transcription	Esophagus	oesophagus
8	chr7:149536400-149556400	Weak transcription	Colonic Mucosa	Colon
9	chr7:149536600-149542800	Weak transcription	Primary B cells from cord blood	blood
10	chr7:149536600-149551600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr7:149536800-149544600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr7:149536800-149544800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr7:149536800-149544800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr7:149536800-149545000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr7:149536800-149545000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr7:149536800-149551400	Weak transcription	HSMMtube	muscle
17	chr7:149536800-149556400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr7:149537000-149543600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr7:149537000-149543800	Weak transcription	Liver	Liver
20	chr7:149537000-149544800	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr7:149537000-149544800	Weak transcription	Fetal Intestine Small	intestine
22	chr7:149537000-149545000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:149537000-149545000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr7:149537000-149545000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr7:149537000-149545000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr7:149537000-149545400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr7:149537000-149551400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr7:149537000-149551400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr7:149537000-149551400	Weak transcription	Fetal Kidney	kidney
30	chr7:149537000-149551400	Weak transcription	Fetal Lung	lung
31	chr7:149537000-149551600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:149537000-149551600	Weak transcription	Gastric	stomach
33	chr7:149537000-149551600	Weak transcription	NHEK	skin
34	chr7:149537000-149551800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr7:149537000-149552000	Weak transcription	NHDF-Ad	bronchial
36	chr7:149537000-149556800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr7:149537200-149542600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr7:149537200-149543000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr7:149537200-149543400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr7:149537200-149544800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr7:149537200-149545200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr7:149537200-149545400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr7:149537200-149551400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr7:149537200-149551800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr7:149539800-149551200	Weak transcription	Fetal Heart	heart
46	chr7:149540000-149543200	Weak transcription	Brain Angular Gyrus	brain
47	chr7:149540000-149546400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr7:149540000-149551600	Weak transcription	Pancreas	Pancrea
49	chr7:149540000-149551800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr7:149540000-149569600	Weak transcription	Psoas Muscle	Psoas

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