Variant report

Variant	rs11580557
Chromosome Location	chr1:211809408-211809409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr1:211809175-211809443	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr1:211809178-211809508	MCF10A-Er-Src	breast:	n/a	n/a
3	SMARCC1	chr1:211809200-211810986	Hela-S3	cervix:	n/a	n/a
4	GTF3C2	chr1:211808656-211810403	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr1:211809165-211809572	IMR90	lung:	n/a	n/a
6	STAT3	chr1:211809170-211809490	MCF10A-Er-Src	breast:	n/a	n/a
7	CEBPB	chr1:211809217-211809545	A549	lung:	n/a	n/a
8	SMARCB1	chr1:211809353-211810640	Hela-S3	cervix:	n/a	n/a
9	STAT3	chr1:211809108-211809482	MCF10A-Er-Src	breast:	n/a	n/a
10	CEBPB	chr1:211809083-211809560	Hela-S3	cervix:	n/a	n/a
11	SMC3	chr1:211809351-211809580	Hela-S3	cervix:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:211805499..211810389-chr1:211816053..211819078,4	K562	blood:
2	chr1:211808019..211810498-chr1:211819976..211822363,2	K562	blood:
3	chr1:211788189..211791176-chr1:211807791..211810721,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRAF5-4	chr1:211809248-211809787	XLOC_000549
2	lnc-NEK2-1	chr1:211809248-211809787	ENSG00000228792.2

No data

Variant related genes	Relation type
ENSG00000227764	TF binding region
ENSG00000228792	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10157989	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10158618	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10158723	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10158740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10494940	1.00[JPT][hapmap]
rs11577181	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590554	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12239534	0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12711504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711505	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711506	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711507	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730869	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12749444	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12751564	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12755496	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12756676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17017855	1.00[ASN][1000 genomes]
rs17651870	1.00[JPT][hapmap]
rs34028707	0.95[ASN][1000 genomes]
rs4345851	0.81[ASN][1000 genomes]
rs4399227	0.81[ASN][1000 genomes]
rs4562684	0.81[ASN][1000 genomes]
rs4951414	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4951417	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4951420	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs603227	1.00[JPT][hapmap]
rs6540692	0.81[ASN][1000 genomes]
rs7529914	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765202	0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010919	chr1:211804252-211823073	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211804200-211813400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:211804200-211816600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:211806800-211809600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr1:211806800-211809600	Weak transcription	Fetal Intestine Small	intestine
5	chr1:211806800-211811600	Weak transcription	Fetal Intestine Large	intestine
6	chr1:211806800-211813000	Weak transcription	Stomach Mucosa	stomach
7	chr1:211807000-211809600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:211807000-211810600	Weak transcription	Placenta	Placenta
9	chr1:211807000-211811600	Weak transcription	Esophagus	oesophagus
10	chr1:211807000-211812000	Weak transcription	Adipose Nuclei	Adipose
11	chr1:211807000-211816200	Weak transcription	Colonic Mucosa	Colon
12	chr1:211807000-211816200	Weak transcription	Ovary	ovary
13	chr1:211807200-211809600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:211807200-211809800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:211807200-211812000	Weak transcription	NHLF	lung
16	chr1:211807200-211816600	Weak transcription	Right Ventricle	heart
17	chr1:211807200-211817200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:211807400-211810000	Weak transcription	Spleen	Spleen
19	chr1:211807400-211812200	Weak transcription	NH-A	brain
20	chr1:211807400-211816800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:211807600-211811600	Weak transcription	Liver	Liver
22	chr1:211807600-211812800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:211807600-211812800	Weak transcription	Pancreas	Pancrea
24	chr1:211807600-211813000	Weak transcription	HSMMtube	muscle
25	chr1:211807600-211816600	Weak transcription	Left Ventricle	heart
26	chr1:211807800-211809600	Weak transcription	HMEC	breast
27	chr1:211808000-211810000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:211808600-211810800	Enhancers	Osteobl	bone
29	chr1:211808800-211810600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:211809200-211810200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:211809200-211810400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:211809400-211809800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:211809400-211809800	Flanking Active TSS	Hela-S3	cervix
34	chr1:211809400-211810200	Enhancers	HSMM	muscle
35	chr1:211809400-211810200	Enhancers	NHDF-Ad	bronchial
36	chr1:211809400-211810800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:211809400-211810800	Enhancers	Muscle Satellite Cultured Cells	--
38	chr1:211809400-211810800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:211809400-211811200	Enhancers	HepG2	liver
40	chr1:211809400-211813000	Enhancers	A549	lung

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