Variant report

Variant	rs12001073
Chromosome Location	chr9:95994699-95994700
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	ZNF143	chr9:95994540-95994753	H1-hESC	embryonic stem cell:	n/a	n/a
3	EP300	chr9:95994618-95995468	ECC-1	luminal epithelium:	n/a	n/a
4	NFIC	chr9:95994688-95995357	ECC-1	luminal epithelium:	n/a	n/a
5	TCF12	chr9:95994486-95995475	ECC-1	luminal epithelium:	n/a	chr9:95995001-95995008

No.	Distal block	Cell Line	Cell type
1	chr9:95985503..95987734-chr9:95991883..95994859,2	K562	blood:
2	chr9:95993583..95995439-chr9:95997660..95999567,2	MCF-7	breast:
3	chr9:95959322..95962228-chr9:95991755..95995134,3	MCF-7	breast:
4	chr9:95896382..95898077-chr9:95992649..95994936,2	MCF-7	breast:

Variant related genes	Relation type
WNK2	TF binding region
ENSG00000131669	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10992681	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1107614	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1107615	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11787888	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11790795	0.82[CEU][hapmap]
rs11793893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12000967	0.81[EUR][1000 genomes]
rs12002458	0.83[AMR][1000 genomes]
rs13287544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13290796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13301530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34085543	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34834050	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35199621	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35438673	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4329328	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7019910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022051	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7046965	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7855391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857220	0.81[EUR][1000 genomes]
rs7867954	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7873162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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

No data

Chromatin state (count:48 , 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	chr9:95987400-95994800	Weak transcription	Psoas Muscle	Psoas
7	chr9:95987400-95995000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr9:95987400-96001000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:95987400-96005200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:95988200-96006800	Weak transcription	Esophagus	oesophagus
11	chr9:95988400-95999800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr9:95988600-95997200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:95990800-95995000	Enhancers	Colonic Mucosa	Colon
14	chr9:95991200-95994800	Strong transcription	HepG2	liver
15	chr9:95991200-95995200	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr9:95992200-95995200	Enhancers	Stomach Mucosa	stomach
17	chr9:95992200-95999800	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:95992600-95995200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr9:95993000-95995000	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr9:95993200-95995000	Bivalent Enhancer	Fetal Stomach	stomach
21	chr9:95993400-95995000	Enhancers	Left Ventricle	heart
22	chr9:95993400-95995000	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr9:95993600-95995000	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr9:95993600-95997600	Weak transcription	Fetal Lung	lung
25	chr9:95993600-96005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:95993800-95995400	Genic enhancers	Fetal Intestine Small	intestine
27	chr9:95993800-95997400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:95993800-96001800	Weak transcription	Spleen	Spleen
29	chr9:95994000-95994800	Strong transcription	Brain Germinal Matrix	brain
30	chr9:95994000-95995000	Strong transcription	Fetal Brain Female	brain
31	chr9:95994000-95996400	Weak transcription	Placenta	Placenta
32	chr9:95994000-95997200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr9:95994000-95997400	Weak transcription	Fetal Heart	heart
34	chr9:95994000-96001000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr9:95994200-95995200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr9:95994200-95995200	Genic enhancers	Fetal Intestine Large	intestine
37	chr9:95994200-95996800	Weak transcription	Right Ventricle	heart
38	chr9:95994200-95997200	Weak transcription	Brain Anterior Caudate	brain
39	chr9:95994400-95995200	Enhancers	H1 Cell Line	embryonic stem cell
40	chr9:95994400-95996400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr9:95994400-95997200	Weak transcription	Brain Hippocampus Middle	brain
42	chr9:95994600-95994800	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr9:95994600-95994800	Genic enhancers	Stomach Smooth Muscle	stomach
44	chr9:95994600-95995000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr9:95994600-95995400	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr9:95994600-95996400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr9:95994600-95997400	Weak transcription	Brain Substantia Nigra	brain
48	chr9:95994600-95997600	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links