Variant report

Variant	rs7041398
Chromosome Location	chr9:95995159-95995160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXM1	chr9:95994681-95995452	ECC-1	luminal epithelium:	n/a	n/a
2	EP300	chr9:95994751-95995390	ECC-1	luminal epithelium:	n/a	n/a
3	MAX	chr9:95994803-95995320	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr9:95994711-95995204	ECC-1	luminal epithelium:	n/a	n/a
5	ESR1	chr9:95994879-95995235	ECC-1	luminal epithelium:	n/a	n/a
6	USF1	chr9:95994778-95995307	ECC-1	luminal epithelium:	n/a	n/a
7	NFIC	chr9:95994729-95995373	ECC-1	luminal epithelium:	n/a	n/a
8	EP300	chr9:95994618-95995468	ECC-1	luminal epithelium:	n/a	n/a
9	NFIC	chr9:95994688-95995357	ECC-1	luminal epithelium:	n/a	n/a
10	TCF12	chr9:95994486-95995475	ECC-1	luminal epithelium:	n/a	chr9:95995001-95995008
11	RAD21	chr9:95994777-95995255	ECC-1	luminal epithelium:	n/a	n/a
12	MAX	chr9:95994753-95995345	ECC-1	luminal epithelium:	n/a	n/a
13	TCF12	chr9:95994772-95995441	ECC-1	luminal epithelium:	n/a	chr9:95995001-95995008

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95993583..95995439-chr9:95997660..95999567,2	MCF-7	breast:

No data

Variant related genes	Relation type
WNK2	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10739945	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs10761210	0.92[TSI][hapmap]
rs10992685	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992686	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992701	0.80[JPT][hapmap];0.96[TSI][hapmap]
rs11788911	0.84[CEU][hapmap];0.94[CHB][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11790111	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12683147	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34795796	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4617217	1.00[ASW][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs56154239	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7029773	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031132	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7032194	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7048527	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7865467	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9696691	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][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
rs7041398	PTCH1	cis	cerebellum	SCAN
rs7041398	GADD45G	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95984800-95998000	Enhancers	Pancreas	Pancrea
2	chr9:95986200-96006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:95987200-95996800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:95987200-95997200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr9:95987200-96000200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:95987400-96001000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr9:95987400-96005200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:95988200-96006800	Weak transcription	Esophagus	oesophagus
9	chr9:95988400-95999800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:95988600-95997200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr9:95991200-95995200	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr9:95992200-95995200	Enhancers	Stomach Mucosa	stomach
13	chr9:95992200-95999800	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:95992600-95995200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr9:95993600-95997600	Weak transcription	Fetal Lung	lung
16	chr9:95993600-96005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:95993800-95995400	Genic enhancers	Fetal Intestine Small	intestine
18	chr9:95993800-95997400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr9:95993800-96001800	Weak transcription	Spleen	Spleen
20	chr9:95994000-95996400	Weak transcription	Placenta	Placenta
21	chr9:95994000-95997200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:95994000-95997400	Weak transcription	Fetal Heart	heart
23	chr9:95994000-96001000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr9:95994200-95995200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr9:95994200-95995200	Genic enhancers	Fetal Intestine Large	intestine
26	chr9:95994200-95996800	Weak transcription	Right Ventricle	heart
27	chr9:95994200-95997200	Weak transcription	Brain Anterior Caudate	brain
28	chr9:95994400-95995200	Enhancers	H1 Cell Line	embryonic stem cell
29	chr9:95994400-95996400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr9:95994400-95997200	Weak transcription	Brain Hippocampus Middle	brain
31	chr9:95994600-95995400	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr9:95994600-95996400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr9:95994600-95997400	Weak transcription	Brain Substantia Nigra	brain
34	chr9:95994600-95997600	Weak transcription	Gastric	stomach
35	chr9:95994800-95995200	Enhancers	Psoas Muscle	Psoas
36	chr9:95994800-95996800	Weak transcription	Brain Germinal Matrix	brain
37	chr9:95994800-95997000	Weak transcription	Brain Angular Gyrus	brain
38	chr9:95994800-95997000	Weak transcription	HepG2	liver
39	chr9:95994800-95997400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:95995000-95995200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr9:95995000-95995200	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr9:95995000-95995200	Genic enhancers	Stomach Smooth Muscle	stomach
43	chr9:95995000-95996200	Weak transcription	Fetal Brain Female	brain
44	chr9:95995000-95996200	Weak transcription	Fetal Stomach	stomach
45	chr9:95995000-95996200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr9:95995000-95996400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr9:95995000-95996600	Weak transcription	Left Ventricle	heart
48	chr9:95995000-95996800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr9:95995000-95996800	Weak transcription	Colonic Mucosa	Colon

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