Variant report

Variant	rs62555451
Chromosome Location	chr9:22217486-22217487
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TFAP2A	chr9:22216602-22217570	Hela-S3	cervix:	n/a	chr9:22217013-22217028
2	GTF2F1	chr9:22216579-22217676	Hela-S3	cervix:	n/a	n/a
3	SMC3	chr9:22216408-22217509	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr9:22216672-22217630	Hela-S3	cervix:	n/a	n/a
5	TFAP2C	chr9:22216609-22217634	Hela-S3	cervix:	n/a	n/a
6	ELK1	chr9:22217413-22217694	Hela-S3	cervix:	n/a	n/a
7	CHD2	chr9:22216557-22217677	Hela-S3	cervix:	n/a	n/a
8	RCOR1	chr9:22216668-22217565	Hela-S3	cervix:	n/a	n/a
9	USF2	chr9:22216763-22217569	Hela-S3	cervix:	n/a	n/a
10	MAX	chr9:22216664-22217540	Hela-S3	cervix:	n/a	n/a
11	TCF7L2	chr9:22216665-22217610	Hela-S3	cervix:	n/a	n/a
12	TCF7L2	chr9:22216673-22217648	HCT-116	colon:	n/a	n/a
13	JUND	chr9:22216767-22217586	Hela-S3	cervix:	n/a	chr9:22217037-22217048
14	TBP	chr9:22216752-22217531	Hela-S3	cervix:	n/a	n/a
15	JUN	chr9:22216790-22217581	Hela-S3	cervix:	n/a	n/a
16	MXI1	chr9:22216726-22217603	Hela-S3	cervix:	n/a	n/a
17	RAD21	chr9:22216551-22217597	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:22139628..22142458-chr9:22215449..22217635,2	MCF-7	breast:
2	chr9:22146078..22148525-chr9:22216609..22218568,2	MCF-7	breast:
3	chr9:22216075..22219047-chr9:22230410..22232299,2	MCF-7	breast:
4	chr9:22106947..22109176-chr9:22216532..22218954,2	MCF-7	breast:
5	chr9:22101148..22103535-chr9:22215387..22218852,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000236921	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11788928	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11790978	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11792798	0.90[EUR][1000 genomes]
rs11792897	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11792932	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12003808	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16905769	1.00[EUR][1000 genomes]
rs2025797	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2383209	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2383212	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2383213	0.82[EUR][1000 genomes]
rs4461984	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4540492	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4621906	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4644346	0.95[EUR][1000 genomes]
rs62555449	0.85[EUR][1000 genomes]
rs62555450	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62555452	0.95[EUR][1000 genomes]
rs62555453	0.90[EUR][1000 genomes]
rs62555455	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62559460	0.95[EUR][1000 genomes]
rs62559467	0.95[EUR][1000 genomes]
rs62559468	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62559469	0.95[EUR][1000 genomes]
rs62559470	0.95[EUR][1000 genomes]
rs62559471	0.95[EUR][1000 genomes]
rs62559472	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62559473	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62559474	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62559475	0.95[EUR][1000 genomes]
rs62559493	0.87[EUR][1000 genomes]
rs62559494	0.82[EUR][1000 genomes]
rs62559495	0.82[EUR][1000 genomes]
rs6475620	0.90[EUR][1000 genomes]
rs7035115	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73442947	0.90[EUR][1000 genomes]
rs73444955	0.95[EUR][1000 genomes]
rs736723	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7848967	0.90[EUR][1000 genomes]
rs7853527	0.82[EUR][1000 genomes]
rs7853566	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859353	1.00[EUR][1000 genomes]
rs7859407	0.95[EUR][1000 genomes]
rs7872728	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs943399	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv892749	chr9:22125913-22244280	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1021264	chr9:22159622-22293804	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1033789	chr9:22183150-22266091	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1029289	chr9:22193167-23023688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1016067	chr9:22210874-22432654	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1015364	chr9:22211364-22416886	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv540086	chr9:22211364-22416886	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22208800-22218000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:22209400-22217600	Enhancers	NHDF-Ad	bronchial
3	chr9:22209400-22218400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr9:22212800-22220200	Strong transcription	A549	lung
5	chr9:22214200-22217600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:22215200-22219000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr9:22216200-22217800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr9:22216400-22218400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:22216800-22217600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:22216800-22217600	Enhancers	NH-A	brain
11	chr9:22217000-22219000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:22217200-22217800	Flanking Active TSS	HSMMtube	muscle
13	chr9:22217400-22217800	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links