Variant report

Variant	rs11790900
Chromosome Location	chr9:101568727-101568728
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	CTCF	chr9:101568715-101568924	Hela-S3	cervix:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
2	CTCF	chr9:101568700-101568850	BJ	skin:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
3	CTCF	chr9:101568695-101568972	GM12878	blood:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
4	CTCF	chr9:101568580-101568730	GM12873	blood:	n/a	n/a
5	CTCF	chr9:101568510-101570694	A549	lung:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
6	RAD21	chr9:101568647-101569113	A549	lung:	n/a	chr9:101568821-101568840
7	CTCF	chr9:101568720-101568870	Hela-S3	cervix:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
8	CTCF	chr9:101568720-101568870	AG09319	gingival:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
9	MYC	chr9:101568700-101568842	MCF10A-Er-Src	breast:	n/a	n/a
10	CTCF	chr9:101568720-101568870	HRPEpiC	eye:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
11	CTCF	chr9:101568530-101569186	HCT-116	colon:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
12	CTCF	chr9:101568670-101568990	IMR90	lung:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
13	SMC3	chr9:101568691-101568951	Hela-S3	cervix:	n/a	chr9:101568822-101568836
14	CTCF	chr9:101568700-101568850	HCPEpiC	choroid plexus:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
15	CTCF	chr9:101568660-101568810	HAc	cerebellar:	n/a	n/a
16	RAD21	chr9:101568712-101568941	IMR90	lung:	n/a	chr9:101568821-101568840
17	CTCF	chr9:101568660-101568810	AG04450	lung:	n/a	n/a
18	CTCF	chr9:101568622-101569070	MCF-7	breast:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
19	CTCF	chr9:101568721-101568924	LNCaP	prostate:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
20	CTCF	chr9:101568680-101568830	GM12872	blood:	n/a	n/a
21	RAD21	chr9:101568541-101569168	HCT-116	colon:	n/a	chr9:101568821-101568840
22	CTCF	chr9:101568680-101568830	BE2_C	brain:	n/a	n/a
23	CTCF	chr9:101568700-101568850	HMEC	breast:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
24	CTCF	chr9:101568700-101568850	WERI-Rb-1	eye:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
25	RAD21	chr9:101568663-101568993	Hela-S3	cervix:	n/a	chr9:101568821-101568840
26	CTCF	chr9:101568640-101568790	HCM	heart:	n/a	n/a
27	CTCF	chr9:101568660-101568810	HCT-116	colon:	n/a	n/a
28	CTCF	chr9:101568660-101568810	AG09309	skin:	n/a	n/a
29	CTCF	chr9:101568705-101568933	HUVEC	blood vessel:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
30	CTCF	chr9:101568614-101569057	A549	lung:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
31	RAD21	chr9:101568496-101569167	SK-N-SH	brain:	n/a	chr9:101568821-101568840
32	CTCF	chr9:101568720-101568870	SK-N-SH_RA	brain:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
33	CTCF	chr9:101568695-101569079	MCF-7	breast:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
34	CTCF	chr9:101568700-101568850	Hela-S3	cervix:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
35	CTCF	chr9:101568720-101568870	NHDF-neo	bronchial:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
36	CTCF	chr9:101568693-101568877	A549	lung:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
37	CTCF	chr9:101568720-101568870	HVMF	connective:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
38	CTCF	chr9:101568720-101568870	GM06990	blood:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
39	CTCF	chr9:101568670-101568908	SK-N-SH_RA	brain:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
40	RAD21	chr9:101568718-101568958	SK-N-SH_RA	brain:	n/a	chr9:101568821-101568840
41	CTCF	chr9:101568720-101568870	AoAF	blood vessel:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
42	CTCF	chr9:101568664-101568992	K562	blood:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
43	CTCF	chr9:101568720-101568870	MCF-7	breast:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
44	CTCF	chr9:101568660-101568810	A549	lung:	n/a	n/a
45	CTCF	chr9:101568720-101568870	HCPEpiC	choroid plexus:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
46	CTCF	chr9:101568720-101568870	NHLF	lung:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
47	CTCF	chr9:101568700-101568850	HL-60	blood:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
48	CTCF	chr9:101568720-101568870	HPAF	blood vessel:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
49	RAD21	chr9:101568701-101569012	MCF-7	breast:	n/a	chr9:101568821-101568840
50	CTCF	chr9:101568720-101568870	BJ	skin:	n/a	chr9:101568822-101568843 chr9:101568820-101568838

No.	Distal block	Cell Line	Cell type
1	chr9:101567600..101569220-chr9:101571487..101573916,3	MCF-7	breast:
2	chr9:101568546..101571235-chr9:101609367..101611059,3	MCF-7	breast:
3	chr9:101568383..101569041-chr9:101610796..101611367,2	MCF-7	breast:
4	chr9:101567740..101569488-chr9:101580448..101582310,2	K562	blood:
5	chr9:101556573..101560424-chr9:101566029..101574080,12	MCF-7	breast:
6	chr9:101550194..101555244-chr9:101566657..101571786,8	MCF-7	breast:
7	chr9:101551293..101553847-chr9:101568036..101571328,4	K562	blood:
8	chr9:101555483..101562112-chr9:101568669..101573087,9	K562	blood:
9	chr9:101557242..101560519-chr9:101566443..101572716,8	MCF-7	breast:
10	chr9:101568251..101569109-chr9:101760833..101761361,2	MCF-7	breast:

Variant related genes	Relation type
GALNT12	TF binding region
ENSG00000165138	Chromatin interaction
ENSG00000119514	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11787982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11788506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11788953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11789133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11791355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11791408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11792301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11792605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11793007	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11793365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11794260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11794814	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11794957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11795201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28397053	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28512311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35229220	1.00[EUR][1000 genomes]
rs41283626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41283630	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45543535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57882865	1.00[ASN][1000 genomes]
rs61025806	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61335015	1.00[ASN][1000 genomes]
rs73491756	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv893614	chr9:101340316-101671634	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv893615	chr9:101356515-101678036	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101559600-101569000	Weak transcription	Pancreas	Pancrea
2	chr9:101559600-101569600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:101562600-101569400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:101565400-101569000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:101566200-101569200	Weak transcription	Fetal Stomach	stomach
6	chr9:101567200-101568800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr9:101567400-101569200	Weak transcription	Fetal Lung	lung
8	chr9:101567400-101569400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr9:101567400-101569400	Enhancers	Fetal Intestine Small	intestine
10	chr9:101567400-101569400	Enhancers	K562	blood
11	chr9:101567400-101569600	Enhancers	HMEC	breast
12	chr9:101567600-101569200	Enhancers	Colonic Mucosa	Colon
13	chr9:101567600-101569400	Enhancers	Duodenum Mucosa	Duodenum
14	chr9:101567600-101569400	Enhancers	Esophagus	oesophagus
15	chr9:101567600-101569400	Enhancers	Fetal Intestine Large	intestine
16	chr9:101567600-101569600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:101567600-101569600	Enhancers	Gastric	stomach
18	chr9:101567600-101569600	Enhancers	NHEK	skin
19	chr9:101567600-101570000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:101567800-101568800	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr9:101567800-101569000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:101567800-101569400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:101567800-101569400	Weak transcription	Right Ventricle	heart
24	chr9:101567800-101569400	Enhancers	Stomach Mucosa	stomach
25	chr9:101567800-101569800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:101567800-101569800	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr9:101568000-101569200	Weak transcription	Spleen	Spleen
28	chr9:101568000-101569400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:101568200-101569000	Enhancers	Colon Smooth Muscle	Colon
30	chr9:101568200-101569800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr9:101568400-101568800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:101568400-101569200	Enhancers	Fetal Brain Male	brain
33	chr9:101568400-101570600	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr9:101568600-101569000	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr9:101568600-101569200	Active TSS	Rectal Smooth Muscle	rectum
36	chr9:101568600-101569200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr9:101568600-101569400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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