Variant report

Variant	rs6545531
Chromosome Location	chr2:56183756-56183757
allele	C/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	GATA3	chr2:56183731-56184024	T-47D	breast:	n/a	n/a
2	FOXA1	chr2:56183707-56184106	T-47D	breast:	n/a	chr2:56183950-56183965
3	POLR2A	chr2:56183741-56184694	HUVEC	blood vessel:	n/a	n/a
4	EP300	chr2:56183750-56184073	T-47D	breast:	n/a	chr2:56183955-56183965
5	FOXA1	chr2:56183746-56184073	T-47D	breast:	n/a	chr2:56183950-56183965

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:56174984..56177810-chr2:56181564..56184235,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EFEMP1-1	chr2:56183727-56185924	NONHSAT070812

Variant related genes	Relation type
RN7SKP208	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10185077	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10192259	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11125611	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12472832	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13431149	0.96[ASN][1000 genomes]
rs1432560	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1432561	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1432563	0.97[ASN][1000 genomes]
rs1432564	0.96[ASN][1000 genomes]
rs1465685	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1583266	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1583267	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1897478	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2278366	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2868984	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34552760	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3972318	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4453721	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4635565	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4672080	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4672081	0.97[ASN][1000 genomes]
rs4672082	0.97[ASN][1000 genomes]
rs55805406	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6704991	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6721145	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6724998	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6733881	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6733889	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6747490	0.96[ASN][1000 genomes]
rs724539	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs724540	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7422809	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7561395	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7561417	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7564964	0.97[ASN][1000 genomes]
rs981037	0.96[ASN][1000 genomes]

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	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	nsv874161	chr2:56154316-56203798	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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
4	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:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56171000-56185000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:56178000-56185200	Weak transcription	Right Atrium	heart
3	chr2:56180000-56188800	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:56180200-56183800	Weak transcription	Ovary	ovary
5	chr2:56182400-56185200	Weak transcription	NH-A	brain
6	chr2:56182600-56184000	Weak transcription	Hela-S3	cervix
7	chr2:56182600-56185000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr2:56182600-56185200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:56182600-56185400	Weak transcription	Fetal Lung	lung
10	chr2:56182800-56183800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:56182800-56183800	Weak transcription	Osteobl	bone
12	chr2:56182800-56184000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:56182800-56184200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:56182800-56184200	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links