Variant report

Variant	rs12532428
Chromosome Location	chr7:39894883-39894884
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:55)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:55 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:39894610-39894919	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr7:39894672-39894890	GM12891	blood:	n/a	n/a
3	POLR2A	chr7:39894524-39895092	A549	lung:	n/a	n/a
4	CTCF	chr7:39894719-39894896	Fibrobl	skin:	n/a	n/a
5	POLR2A	chr7:39894448-39895090	GM12892	blood:	n/a	n/a
6	PAX5	chr7:39894646-39894901	GM12878	blood:	n/a	n/a
7	POLR2A	chr7:39894625-39895009	HepG2	liver:	n/a	n/a
8	POLR2A	chr7:39894628-39894910	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr7:39894515-39895119	ProgFib	skin:	n/a	n/a
10	POLR2A	chr7:39894578-39894893	U87	brain:	n/a	n/a
11	POLR2A	chr7:39894510-39895027	GM12892	blood:	n/a	n/a
12	POLR2A	chr7:39894556-39895087	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr7:39894576-39894939	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr7:39894583-39895092	K562	blood:	n/a	n/a
15	PAX5	chr7:39894598-39894885	GM12878	blood:	n/a	n/a
16	TAF1	chr7:39894660-39894976	GM12878	blood:	n/a	n/a
17	POLR2A	chr7:39894495-39894945	SK-N-MC	brain:	n/a	n/a
18	EBF1	chr7:39894616-39894883	GM12878	blood:	n/a	n/a
19	POLR2A	chr7:39894565-39895074	Hela-S3	cervix:	n/a	n/a
20	EBF1	chr7:39894560-39894953	GM12878	blood:	n/a	n/a
21	TAF1	chr7:39894564-39894891	HepG2	liver:	n/a	n/a
22	POLR2A	chr7:39894583-39895058	GM12878	blood:	n/a	n/a
23	POLR2A	chr7:39894543-39895018	MCF-7	breast:	n/a	n/a
24	POLR2A	chr7:39894594-39894971	PANC-1	pancreas:	n/a	n/a
25	TAF1	chr7:39894634-39894917	HepG2	liver:	n/a	n/a
26	POLR2A	chr7:39894608-39894886	HepG2	liver:	n/a	n/a
27	TAF1	chr7:39894723-39894919	Hela-S3	cervix:	n/a	n/a
28	TAF1	chr7:39894650-39894911	GM12892	blood:	n/a	n/a
29	POU2F2	chr7:39894617-39894956	GM12891	blood:	n/a	n/a
30	POLR2A	chr7:39894565-39894915	GM12891	blood:	n/a	n/a
31	POU2F2	chr7:39894492-39895006	GM12878	blood:	n/a	n/a
32	POLR2A	chr7:39894584-39894886	A549	lung:	n/a	n/a
33	POLR2A	chr7:39894611-39894929	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr7:39894624-39894942	GM12892	blood:	n/a	n/a
35	POLR2A	chr7:39894565-39894923	U87	brain:	n/a	n/a
36	POLR2A	chr7:39894561-39894892	H1-hESC	embryonic stem cell:	n/a	n/a
37	TAF1	chr7:39894481-39894931	H1-hESC	embryonic stem cell:	n/a	n/a
38	SP1	chr7:39894665-39894923	GM12878	blood:	n/a	n/a
39	POLR2A	chr7:39894544-39895068	MCF-7	breast:	n/a	n/a
40	POLR2A	chr7:39894486-39895120	Gliobla	brain:	n/a	n/a
41	HEY1	chr7:39894546-39894967	K562	blood:	n/a	n/a
42	TAF1	chr7:39894569-39894889	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr7:39894496-39895048	GM12878	blood:	n/a	n/a
44	POLR2A	chr7:39894579-39895046	MCF-7	breast:	n/a	n/a
45	POLR2A	chr7:39894612-39894926	GM12878	blood:	n/a	n/a
46	PBX3	chr7:39894715-39894898	GM12878	blood:	n/a	n/a
47	HEY1	chr7:39894510-39895035	HepG2	liver:	n/a	n/a
48	POLR2A	chr7:39894576-39894956	GM12892	blood:	n/a	n/a
49	POLR2A	chr7:39894578-39894902	SK-N-MC	brain:	n/a	n/a
50	POLR2A	chr7:39894469-39894952	H1-hESC	embryonic stem cell:	n/a	n/a

No data

Variant related genes	Relation type
RWDD4P2	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10246791	0.81[ASN][1000 genomes]
rs10257407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10272635	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10281153	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10951616	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs11561862	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12672010	0.90[ASN][1000 genomes]
rs13438265	0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1880129	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs28639775	0.89[ASN][1000 genomes]
rs3823741	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs4723912	0.90[ASN][1000 genomes]
rs4723913	0.90[ASN][1000 genomes]
rs59418652	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6978120	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs7776988	0.90[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	nsv427777	chr7:39726513-39936904	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv887973	chr7:39772654-40110720	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv887974	chr7:39827400-39956829	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv887975	chr7:39858378-40124137	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
5	nsv887976	chr7:39874986-40018693	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	nsv887977	chr7:39885541-40018693	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12532428	C7orf36	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39894200-39895000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr7:39894200-39895000	Active TSS	Primary hematopoietic stem cells	blood
3	chr7:39894200-39895000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:39894200-39895000	Active TSS	Brain Angular Gyrus	brain
5	chr7:39894200-39895000	Active TSS	Brain Substantia Nigra	brain
6	chr7:39894200-39895000	Bivalent/Poised TSS	Fetal Lung	lung
7	chr7:39894200-39895000	Active TSS	Fetal Muscle Trunk	muscle
8	chr7:39894200-39895000	Active TSS	Right Atrium	heart
9	chr7:39894200-39895000	Active TSS	Right Ventricle	heart
10	chr7:39894200-39895000	Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr7:39894200-39895200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:39894200-39895200	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr7:39894200-39895200	Active TSS	Psoas Muscle	Psoas
14	chr7:39894200-39895200	Bivalent/Poised TSS	NHDF-Ad	bronchial
15	chr7:39894400-39895000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
16	chr7:39894400-39895000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
17	chr7:39894400-39895000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr7:39894400-39895000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:39894400-39895000	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
20	chr7:39894400-39895000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr7:39894400-39895000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:39894400-39895000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:39894400-39895000	Active TSS	Colon Smooth Muscle	Colon
24	chr7:39894400-39895000	Active TSS	Duodenum Mucosa	Duodenum
25	chr7:39894400-39895000	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
26	chr7:39894400-39895000	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr7:39894400-39895000	Active TSS	Fetal Muscle Leg	muscle
28	chr7:39894400-39895000	Active TSS	Fetal Stomach	stomach
29	chr7:39894400-39895000	Active TSS	Ovary	ovary
30	chr7:39894400-39895000	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr7:39894400-39895000	Active TSS	HSMM	muscle
32	chr7:39894400-39895000	Bivalent/Poised TSS	NH-A	brain
33	chr7:39894400-39895000	Bivalent/Poised TSS	Osteobl	bone
34	chr7:39894400-39895200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
35	chr7:39894400-39895200	Active TSS	Muscle Satellite Cultured Cells	--
36	chr7:39894400-39895200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr7:39894400-39895200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr7:39894400-39895200	Active TSS	Adipose Nuclei	Adipose
39	chr7:39894400-39895200	Active TSS	Brain Hippocampus Middle	brain
40	chr7:39894400-39895200	Active TSS	Stomach Smooth Muscle	stomach
41	chr7:39894400-39895200	Bivalent/Poised TSS	HUVEC	blood vessel
42	chr7:39894600-39895000	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr7:39894600-39895000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr7:39894600-39895000	Enhancers	Primary B cells from peripheral blood	blood
45	chr7:39894600-39895000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr7:39894600-39895000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr7:39894600-39895000	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
48	chr7:39894600-39895000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr7:39894600-39895000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr7:39894600-39895000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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