Variant report

Variant	rs11892554
Chromosome Location	chr2:208941965-208941966
allele	A/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	CEBPB	chr2:208941960-208942133	HepG2	liver:	n/a	chr2:208942035-208942046
2	CEBPB	chr2:208941885-208942162	IMR90	lung:	n/a	chr2:208942035-208942046

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:208913270..208916048-chr2:208940472..208942742,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238582	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10932231	0.88[ASN][1000 genomes]
rs10932232	0.87[ASN][1000 genomes]
rs10932233	0.88[ASN][1000 genomes]
rs10932237	0.84[ASN][1000 genomes]
rs10932238	0.97[ASN][1000 genomes]
rs11681747	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11683477	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11694118	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11892539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11894673	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11896152	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11896248	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12465847	0.93[ASN][1000 genomes]
rs12987978	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16840404	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17538082	0.90[CEU][hapmap];0.81[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2123296	0.97[ASN][1000 genomes]
rs34100088	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35306034	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4234085	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4287753	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4673378	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4675729	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4675730	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4675731	0.97[ASN][1000 genomes]
rs62192797	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6711974	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6723206	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6727089	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6727122	0.95[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6735060	0.97[ASN][1000 genomes]
rs6746998	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7422654	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7422655	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs896637	0.95[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	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv2760541	chr2:208936949-208945639	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11892554	PLEKHM3	cis	parietal	SCAN
rs11892554	FZD5	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208941400-208942000	Enhancers	Placenta	Placenta
2	chr2:208941600-208942800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:208941800-208942400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:208941800-208942400	Enhancers	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links