Variant report

Variant	rs1432553
Chromosome Location	chr2:56220271-56220272
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	EP300	chr2:56219221-56220328	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr2:56218058-56220673	HUVEC	blood vessel:	n/a	n/a
3	FOSL2	chr2:56219312-56220394	A549	lung:	n/a	chr2:56219826-56219833 chr2:56219825-56219833
4	JUND	chr2:56219386-56220370	Hela-S3	cervix:	n/a	chr2:56219826-56219833 chr2:56219825-56219833
5	TCF12	chr2:56219215-56220363	A549	lung:	n/a	n/a
6	GATA3	chr2:56219237-56220278	SK-N-SH	brain:	n/a	chr2:56219798-56219807 chr2:56219789-56219806 chr2:56219798-56219808 chr2:56219800-56219807 chr2:56219793-56219814 chr2:56219743-56219756 chr2:56219800-56219810
7	JUND	chr2:56218944-56220314	SK-N-SH	brain:	n/a	chr2:56219826-56219833 chr2:56219825-56219833
8	POLR2A	chr2:56219411-56220592	HUVEC	blood vessel:	n/a	n/a
9	RFX5	chr2:56219236-56220327	Hela-S3	cervix:	n/a	n/a
10	EP300	chr2:56219136-56220322	A549	lung:	n/a	n/a
11	GATA3	chr2:56219088-56220328	SK-N-SH	brain:	n/a	chr2:56219798-56219807 chr2:56219789-56219806 chr2:56219798-56219808 chr2:56219800-56219807 chr2:56219793-56219814 chr2:56219743-56219756 chr2:56219800-56219810
12	EP300	chr2:56219262-56220354	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr2:56219107-56220630	HUVEC	blood vessel:	n/a	n/a
14	JUND	chr2:56219296-56220272	SK-N-SH	brain:	n/a	chr2:56219826-56219833 chr2:56219825-56219833
15	TCF12	chr2:56219131-56220400	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr2:56218938-56220680	HUVEC	blood vessel:	n/a	n/a
17	NFIC	chr2:56219137-56220372	SK-N-SH	brain:	n/a	chr2:56219489-56219505
18	GATA3	chr2:56219105-56220365	A549	lung:	n/a	chr2:56219798-56219807 chr2:56219789-56219806 chr2:56219798-56219808 chr2:56219800-56219807 chr2:56219793-56219814 chr2:56219743-56219756 chr2:56219800-56219810
19	POLR2A	chr2:56219246-56221775	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
MIR216A	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1017371	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10194204	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10194401	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10200414	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10206522	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10206619	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11690813	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11891825	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11893449	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11903947	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11904173	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12713312	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13029542	0.83[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13398053	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13410155	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13431392	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13432828	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1835897	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2009613	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs34561537	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4999828	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545535	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545536	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545537	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545538	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6724635	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6724872	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6745615	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6756818	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7557630	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7601814	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][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	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56217000-56223200	Enhancers	HUVEC	blood vessel
2	chr2:56217200-56222800	Weak transcription	Pancreas	Pancrea
3	chr2:56218000-56220400	Enhancers	HSMMtube	muscle
4	chr2:56218000-56222400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:56218400-56221000	Enhancers	Hela-S3	cervix
6	chr2:56218400-56221200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr2:56218400-56222200	Enhancers	HSMM	muscle
8	chr2:56218400-56223000	Enhancers	Muscle Satellite Cultured Cells	--
9	chr2:56218600-56220600	Enhancers	NH-A	brain
10	chr2:56218600-56221200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:56218800-56220400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:56218800-56220600	Enhancers	NHDF-Ad	bronchial
13	chr2:56218800-56220600	Enhancers	Osteobl	bone
14	chr2:56219000-56221000	Enhancers	NHLF	lung
15	chr2:56219000-56221200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:56219000-56221200	Enhancers	HMEC	breast
17	chr2:56219600-56220400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:56219600-56220600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:56219600-56222000	Enhancers	Fetal Stomach	stomach
20	chr2:56220000-56220400	Flanking Active TSS	A549	lung
21	chr2:56220000-56220600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:56220000-56222000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:56220000-56222200	Weak transcription	Colon Smooth Muscle	Colon

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