Variant report

Variant	rs12506662
Chromosome Location	chr4:87861476-87861477
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:87860692-87861639	GM12878	blood:	n/a	n/a
2	EP300	chr4:87860737-87861509	GM12878	blood:	n/a	n/a
3	WRNIP1	chr4:87860866-87861687	GM12878	blood:	n/a	n/a
4	RELA	chr4:87860392-87861533	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:87860656-87861476	GM18505	blood:	n/a	n/a
6	FOXM1	chr4:87860630-87861547	GM12878	blood:	n/a	n/a
7	CEBPB	chr4:87861438-87861728	IMR90	lung:	n/a	n/a
8	BCLAF1	chr4:87860616-87861590	GM12878	blood:	n/a	n/a
9	PML	chr4:87860666-87861616	GM12878	blood:	n/a	n/a
10	MTA3	chr4:87860076-87862059	GM12878	blood:	n/a	n/a
11	STAT5A	chr4:87860642-87861587	GM12878	blood:	n/a	n/a
12	FOXM1	chr4:87860585-87861687	GM12878	blood:	n/a	n/a
13	IKZF1	chr4:87860734-87861570	GM12878	blood:	n/a	n/a
14	UBTF	chr4:87861390-87861555	K562	blood:	n/a	n/a
15	RUNX3	chr4:87860716-87861570	GM12878	blood:	n/a	n/a
16	MYC	chr4:87861461-87861576	K562	blood:	n/a	n/a
17	RELA	chr4:87860739-87861717	GM15510	blood:	n/a	n/a
18	RELA	chr4:87860731-87861585	GM10847	blood:	n/a	n/a
19	POLR2A	chr4:87860698-87861793	GM12878	blood:	n/a	n/a
20	NFATC1	chr4:87860474-87861730	GM12878	blood:	n/a	n/a
21	POLR2A	chr4:87861454-87861530	MCF10A-Er-Src	breast:	n/a	n/a
22	NFATC1	chr4:87860712-87861681	GM12878	blood:	n/a	n/a
23	IRF1	chr4:87861196-87861480	K562	blood:	n/a	n/a
24	NFIC	chr4:87860470-87861608	GM12878	blood:	n/a	n/a
25	MTA3	chr4:87860233-87861554	GM12878	blood:	n/a	n/a
26	ATF2	chr4:87860207-87861524	GM12878	blood:	n/a	n/a
27	SMC3	chr4:87860723-87861491	GM12878	blood:	n/a	n/a
28	ATF2	chr4:87860520-87861503	GM12878	blood:	n/a	n/a
29	BCL3	chr4:87860738-87861678	GM12878	blood:	n/a	n/a
30	RUNX3	chr4:87860309-87861649	GM12878	blood:	n/a	n/a
31	RELA	chr4:87860316-87861552	GM18505	blood:	n/a	n/a
32	POLR2A	chr4:87860818-87861681	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr4:87860683-87861585	GM12878	blood:	n/a	n/a
34	POLR2A	chr4:87860277-87861727	GM12878	blood:	n/a	n/a
35	RELA	chr4:87860461-87861501	GM19099	blood:	n/a	n/a
36	POLR2A	chr4:87860177-87861734	GM12891	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:87859835..87862279-chr4:87865985..87868737,2	MCF-7	breast:
2	chr4:87860517..87862879-chr4:87877524..87879606,2	K562	blood:
3	chr4:87845889..87863516-chr4:87925389..87935181,79	K562	blood:
4	chr4:87853595..87871697-chr4:87924007..87941983,77	K562	blood:
5	chr4:87861386..87863585-chr4:87881486..87883645,2	K562	blood:
6	chr4:87860293..87862516-chr4:87877340..87879546,2	MCF-7	breast:
7	chr4:87853395..87861870-chr4:87925425..87930611,18	MCF-7	breast:

No data

Variant related genes	Relation type
C4orf36	TF binding region
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1447993	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17012186	0.93[ASN][1000 genomes]
rs1868246	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1992876	0.90[ASN][1000 genomes]
rs2442078	0.85[EUR][1000 genomes]
rs2705621	0.92[EUR][1000 genomes]
rs28522052	0.87[ASN][1000 genomes]
rs2869632	0.86[ASN][1000 genomes]
rs2904151	0.86[ASN][1000 genomes]
rs61586576	0.90[ASN][1000 genomes]
rs6419117	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67773101	0.90[ASN][1000 genomes]
rs6836128	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs725030	0.89[ASN][1000 genomes]
rs72613148	0.92[EUR][1000 genomes]
rs72613149	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7671931	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693780	0.83[ASN][1000 genomes]
rs7693889	0.87[ASN][1000 genomes]
rs9996533	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87856600-87861600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:87857400-87861600	Flanking Active TSS	Dnd41	blood
3	chr4:87857600-87882000	Weak transcription	Spleen	Spleen
4	chr4:87857800-87867800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:87857800-87880200	Weak transcription	HSMM	muscle
6	chr4:87858000-87867600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:87858200-87861600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr4:87858200-87861600	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr4:87858200-87862000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr4:87858200-87866800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr4:87858200-87869400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:87858600-87862000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr4:87858600-87862400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr4:87858600-87862400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr4:87858600-87863200	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr4:87858600-87864800	Enhancers	Fetal Thymus	thymus
17	chr4:87858600-87881000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:87858800-87864400	Enhancers	Liver	Liver
19	chr4:87859000-87861600	Enhancers	Colon Smooth Muscle	Colon
20	chr4:87859000-87862200	Enhancers	Fetal Intestine Small	intestine
21	chr4:87859000-87864400	Enhancers	Fetal Intestine Large	intestine
22	chr4:87859200-87865600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:87859400-87861600	Enhancers	Small Intestine	intestine
24	chr4:87859600-87861800	Enhancers	NHEK	skin
25	chr4:87859800-87861600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr4:87859800-87861600	Enhancers	Muscle Satellite Cultured Cells	--
27	chr4:87859800-87861600	Enhancers	Brain Hippocampus Middle	brain
28	chr4:87859800-87861600	Flanking Active TSS	Hela-S3	cervix
29	chr4:87859800-87862200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:87859800-87863600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:87859800-87864000	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr4:87860000-87861600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr4:87860000-87861800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:87860000-87861800	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr4:87860200-87861600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr4:87860200-87861800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:87860200-87861800	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr4:87860200-87861800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:87860200-87863200	Enhancers	Pancreas	Pancrea
40	chr4:87860400-87861600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr4:87860400-87861600	Enhancers	Fetal Lung	lung
42	chr4:87860400-87861600	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr4:87860400-87861800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:87860600-87861600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:87860600-87861800	Enhancers	Duodenum Mucosa	Duodenum
46	chr4:87860600-87861800	Enhancers	Fetal Heart	heart
47	chr4:87860600-87861800	Enhancers	Fetal Kidney	kidney
48	chr4:87860800-87861600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr4:87860800-87861600	Enhancers	Brain Cingulate Gyrus	brain
50	chr4:87860800-87861600	Transcr. at gene 5' and 3'	Placenta	Placenta

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