Variant report

Variant	rs4617217
Chromosome Location	chr9:95988968-95988969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95988443..95991270-chr9:96059116..96061610,2	MCF-7	breast:
2	chr9:95987275..95989530-chr9:96001109..96003124,2	MCF-7	breast:
3	chr9:95987122..95989176-chr9:96004823..96007042,2	MCF-7	breast:
4	chr9:95986232..95989447-chr9:96010468..96012463,3	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10739944	0.81[MEX][hapmap]
rs10739945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10992685	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10992686	1.00[AFR][1000 genomes]
rs11788911	0.81[JPT][hapmap]
rs12683147	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs34795796	0.99[AFR][1000 genomes]
rs56154239	0.99[AFR][1000 genomes]
rs7029773	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs7031132	1.00[ASW][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7032194	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7041398	1.00[ASW][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7048527	1.00[ASW][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7865467	0.99[AFR][1000 genomes]
rs9696691	1.00[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer 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	30 gene(s)	inside rSNPs	diseases
2	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4617217	GADD45G	cis	cerebellum	SCAN
rs4617217	SECISBP2	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95979600-95992200	Enhancers	Left Ventricle	heart
2	chr9:95981600-95989200	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr9:95984800-95998000	Enhancers	Pancreas	Pancrea
4	chr9:95985200-95989000	Enhancers	Rectal Mucosa Donor 29	rectum
5	chr9:95985200-95989400	Enhancers	Right Ventricle	heart
6	chr9:95985200-95990400	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr9:95985400-95989400	Enhancers	Duodenum Mucosa	Duodenum
8	chr9:95986200-96006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:95986600-95990600	Weak transcription	Small Intestine	intestine
10	chr9:95987200-95989400	Enhancers	Fetal Heart	heart
11	chr9:95987200-95990200	Weak transcription	Stomach Mucosa	stomach
12	chr9:95987200-95992000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:95987200-95996800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr9:95987200-95997200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:95987200-96000200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr9:95987400-95989800	Enhancers	Colonic Mucosa	Colon
17	chr9:95987400-95990400	Weak transcription	Gastric	stomach
18	chr9:95987400-95991200	Weak transcription	HepG2	liver
19	chr9:95987400-95991800	Weak transcription	Spleen	Spleen
20	chr9:95987400-95992400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:95987400-95992600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:95987400-95992800	Weak transcription	Brain Germinal Matrix	brain
23	chr9:95987400-95994800	Weak transcription	Psoas Muscle	Psoas
24	chr9:95987400-95995000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr9:95987400-96001000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr9:95987400-96005200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr9:95987800-95989000	Enhancers	Fetal Thymus	thymus
28	chr9:95987800-95989400	Enhancers	Right Atrium	heart
29	chr9:95988200-95989000	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr9:95988200-95991600	Weak transcription	Colon Smooth Muscle	Colon
31	chr9:95988200-95992200	Weak transcription	Fetal Brain Female	brain
32	chr9:95988200-95993200	Weak transcription	Brain Anterior Caudate	brain
33	chr9:95988200-95993200	Enhancers	Fetal Intestine Large	intestine
34	chr9:95988200-95993400	Weak transcription	Brain Hippocampus Middle	brain
35	chr9:95988200-96006800	Weak transcription	Esophagus	oesophagus
36	chr9:95988400-95989000	Genic enhancers	Stomach Smooth Muscle	stomach
37	chr9:95988400-95991200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr9:95988400-95992800	Genic enhancers	Fetal Intestine Small	intestine
39	chr9:95988400-95999800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr9:95988600-95990400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr9:95988600-95990800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr9:95988600-95997200	Weak transcription	Brain Inferior Temporal Lobe	brain

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