Variant report

Variant	rs4777723
Chromosome Location	chr15:93112038-93112039
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11853255	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11853324	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11854603	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11855589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12915111	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1563366	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1563367	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1563368	0.83[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4778009	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4778010	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4778011	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4778013	0.96[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs958991	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][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	nsv948621	chr15:92688981-93158095	Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
4	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS 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	169 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4777723	CHD2	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93106000-93125800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:93106600-93113200	Weak transcription	Fetal Muscle Leg	muscle
3	chr15:93107000-93113200	Weak transcription	Left Ventricle	heart
4	chr15:93111800-93112200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:93112000-93112200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr15:93112000-93115000	Weak transcription	HSMM	muscle

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links