Variant report

Variant	rs4263839
Chromosome Location	chr9:117566440-117566441
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:117564357..117566825-chr9:117567228..117568733,2	MCF-7	breast:
2	chr9:117565521..117568047-chr9:117568256..117570338,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181634	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10114470	0.92[AFR][1000 genomes]
rs10817678	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3810936	0.88[ASW][hapmap];0.93[LWK][hapmap];0.92[AFR][1000 genomes]
rs4366152	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4372078	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6478108	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6478109	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7848647	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant related diseases (count:1)

Disease	PMID	Source
Crohn's disease	18587394	GWAS catalog

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117562000-117568000	Weak transcription	Colon Smooth Muscle	Colon
2	chr9:117562200-117566600	Weak transcription	HSMMtube	muscle
3	chr9:117562200-117568000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:117562400-117567600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:117562400-117568000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:117564800-117568000	Enhancers	Placenta	Placenta
7	chr9:117565000-117566600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
8	chr9:117565000-117567000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:117565000-117568000	Weak transcription	Right Atrium	heart
10	chr9:117565000-117569400	Enhancers	Fetal Lung	lung
11	chr9:117565200-117566800	Enhancers	Fetal Stomach	stomach
12	chr9:117565200-117567000	Enhancers	Gastric	stomach
13	chr9:117565200-117567800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr9:117565200-117568000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr9:117565200-117569800	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr9:117565400-117568200	Enhancers	NHDF-Ad	bronchial
17	chr9:117565400-117568600	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr9:117565600-117566600	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr9:117565600-117566600	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr9:117565600-117566600	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr9:117565600-117566800	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr9:117565600-117566800	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr9:117565600-117567000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:117565600-117568000	Enhancers	Stomach Mucosa	stomach
25	chr9:117565800-117566600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:117565800-117566800	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr9:117565800-117566800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:117565800-117567000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:117565800-117567000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:117565800-117567000	Enhancers	Lung	lung
31	chr9:117565800-117567000	Enhancers	Pancreas	Pancrea
32	chr9:117565800-117567200	Enhancers	Placenta Amnion	Placenta Amnion
33	chr9:117565800-117567400	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr9:117565800-117567400	Enhancers	Ovary	ovary
35	chr9:117565800-117568000	Enhancers	Colonic Mucosa	Colon
36	chr9:117565800-117568000	Enhancers	Osteobl	bone
37	chr9:117565800-117568800	Enhancers	NHLF	lung
38	chr9:117565800-117569000	Enhancers	HepG2	liver
39	chr9:117566000-117566600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr9:117566000-117566600	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr9:117566000-117566600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr9:117566000-117566800	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr9:117566000-117566800	Enhancers	Small Intestine	intestine
44	chr9:117566000-117567200	Flanking Active TSS	Fetal Kidney	kidney
45	chr9:117566000-117567600	Flanking Active TSS	A549	lung
46	chr9:117566000-117567800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr9:117566000-117568000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:117566000-117568000	Weak transcription	Liver	Liver
49	chr9:117566000-117568400	Flanking Active TSS	Fetal Intestine Large	intestine
50	chr9:117566000-117568400	Flanking Active TSS	HUVEC	blood vessel

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