Variant report

Variant	rs7940008
Chromosome Location	chr11:6409477-6409478
allele	C/T
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	CEBPB	chr11:6409141-6409637	IMR90	lung:	n/a	chr11:6409301-6409312
2	HDAC2	chr11:6409232-6409541	HepG2	liver:	n/a	n/a
3	CEBPB	chr11:6409184-6409573	MCF-7	breast:	n/a	chr11:6409301-6409312
4	FOXA2	chr11:6409177-6409557	HepG2	liver:	n/a	n/a
5	FOXA2	chr11:6409092-6409706	A549	lung:	n/a	n/a
6	STAT3	chr11:6409422-6409594	MCF10A-Er-Src	breast:	n/a	n/a
7	EP300	chr11:6409191-6409483	HepG2	liver:	n/a	n/a
8	FOXA1	chr11:6409120-6409549	HepG2	liver:	n/a	n/a
9	SP1	chr11:6408849-6409565	A549	lung:	n/a	n/a
10	CEBPB	chr11:6409040-6409756	A549	lung:	n/a	chr11:6409301-6409312
11	FOXA1	chr11:6409083-6409552	HepG2	liver:	n/a	n/a
12	SP1	chr11:6408921-6409491	A549	lung:	n/a	n/a
13	CEBPB	chr11:6409021-6409681	Hela-S3	cervix:	n/a	chr11:6409301-6409312
14	CEBPB	chr11:6409152-6409596	K562	blood:	n/a	chr11:6409301-6409312
15	MYC	chr11:6408988-6409644	MCF10A-Er-Src	breast:	n/a	n/a
16	CEBPB	chr11:6409160-6409607	MCF-7	breast:	n/a	chr11:6409301-6409312
17	FOXA1	chr11:6409033-6409658	HepG2	liver:	n/a	n/a
18	SP1	chr11:6409166-6409617	HepG2	liver:	n/a	n/a
19	CEBPB	chr11:6409145-6409629	HepG2	liver:	n/a	chr11:6409301-6409312
20	CEBPB	chr11:6409280-6409596	K562	blood:	n/a	chr11:6409301-6409312
21	FOXA1	chr11:6409054-6409550	HepG2	liver:	n/a	n/a
22	GATA1	chr11:6409388-6412069	PBDE	blood:	n/a	n/a
23	TCF12	chr11:6408947-6409565	A549	lung:	n/a	n/a
24	CEBPB	chr11:6409143-6409596	HepG2	liver:	n/a	chr11:6409301-6409312
25	EP300	chr11:6409005-6409508	Hela-S3	cervix:	n/a	n/a
26	TEAD4	chr11:6408989-6409647	HepG2	liver:	n/a	n/a
27	CEBPB	chr11:6409153-6409628	A549	lung:	n/a	chr11:6409301-6409312
28	CEBPB	chr11:6409164-6409544	A549	lung:	n/a	chr11:6409301-6409312
29	CEBPB	chr11:6409345-6409565	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:6408446..6411520-chr11:6632512..6635216,4	K562	blood:
2	chr11:6408815..6414157-chr11:6415408..6420403,9	K562	blood:
3	chr11:6408886..6411627-chr11:6701722..6704947,4	MCF-7	breast:
4	chr11:6408399..6412955-chr11:6499739..6504366,6	K562	blood:

Variant related genes	Relation type
SMPD1	TF binding region
ENSG00000158042	Chromatin interaction
ENSG00000166313	Chromatin interaction
ENSG00000132286	Chromatin interaction
ENSG00000132254	Chromatin interaction
ENSG00000166337	Chromatin interaction
ENSG00000265264	Chromatin interaction

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

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

rs_ID	r²[population]
rs11040879	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11040880	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11040883	1.00[CEU][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603081	1.00[ASN][1000 genomes]
rs11604636	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417813	1.00[ASN][1000 genomes]
rs2723656	0.83[CEU][hapmap]
rs34995289	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4758097	1.00[ASN][1000 genomes]
rs4758415	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72896245	1.00[ASN][1000 genomes]
rs72896248	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72896249	1.00[ASN][1000 genomes]
rs72896251	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72896252	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72896262	1.00[ASN][1000 genomes]
rs7931364	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7932237	0.91[CEU][hapmap];0.89[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7934983	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935228	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935950	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7937560	1.00[ASN][1000 genomes]
rs7950901	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951904	0.83[CEU][hapmap]
rs8164	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv534152	chr11:6282812-6659230	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv1046995	chr11:6339868-6658766	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv553371	chr11:6395690-6434465	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:6400200-6409600	Weak transcription	Colonic Mucosa	Colon
2	chr11:6400800-6410800	Weak transcription	Primary B cells from cord blood	blood
3	chr11:6402800-6410400	Weak transcription	Brain Substantia Nigra	brain
4	chr11:6405400-6411000	Weak transcription	Gastric	stomach
5	chr11:6405600-6410200	Weak transcription	Fetal Heart	heart
6	chr11:6405600-6410600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:6406400-6410000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr11:6406600-6410600	Weak transcription	Thymus	Thymus
9	chr11:6407000-6409600	Weak transcription	Primary T cells from cord blood	blood
10	chr11:6407000-6409800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr11:6407000-6410400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr11:6407000-6410400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr11:6407000-6410400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr11:6407000-6410400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr11:6407200-6410200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr11:6407200-6410400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr11:6407200-6410400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr11:6407200-6410600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr11:6407200-6410600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr11:6407400-6410600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr11:6407400-6410800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr11:6407600-6409600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr11:6408200-6410800	Enhancers	Fetal Intestine Large	intestine
24	chr11:6408200-6410800	Enhancers	Fetal Intestine Small	intestine
25	chr11:6408200-6411000	Enhancers	Stomach Mucosa	stomach
26	chr11:6408400-6409800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:6408600-6409600	Flanking Active TSS	Hela-S3	cervix
28	chr11:6408600-6409800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:6408600-6410600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr11:6408600-6410600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr11:6408600-6410600	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr11:6408600-6410800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr11:6408600-6410800	Enhancers	Liver	Liver
34	chr11:6408600-6410800	Enhancers	Duodenum Mucosa	Duodenum
35	chr11:6408600-6410800	Enhancers	HepG2	liver
36	chr11:6408600-6411000	Enhancers	Muscle Satellite Cultured Cells	--
37	chr11:6408600-6411200	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr11:6408800-6409600	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr11:6408800-6410000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr11:6408800-6410400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:6408800-6410600	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr11:6408800-6410600	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr11:6408800-6410600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:6408800-6410800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr11:6408800-6410800	Enhancers	HUVEC	blood vessel
46	chr11:6408800-6410800	Enhancers	NHEK	skin
47	chr11:6409000-6409600	Flanking Active TSS	Osteobl	bone
48	chr11:6409000-6410800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr11:6409000-6410800	Enhancers	HMEC	breast
50	chr11:6409000-6411000	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links