Variant report

Variant	rs7979096
Chromosome Location	chr12:43002795-43002796
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10785361	0.92[AFR][1000 genomes]
rs10880328	0.92[AFR][1000 genomes]
rs10880332	0.91[AFR][1000 genomes]
rs11610557	0.82[LWK][hapmap];0.81[MEX][hapmap]
rs11611364	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11834039	0.81[MEX][hapmap]
rs12582503	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36055001	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4768019	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4768424	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4768426	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768427	0.92[AFR][1000 genomes]
rs4768430	0.86[AFR][1000 genomes]
rs61924437	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6582406	0.96[AFR][1000 genomes]
rs7965898	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][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	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv832388	chr12:42878328-43087069	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7979096	FZD6	trans	parietal	SCAN
rs7979096	ZCRB1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:43000600-43002800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:43001400-43005200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:43001600-43004200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:43002000-43003000	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr12:43002000-43003000	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr12:43002200-43003000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr12:43002600-43002800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:43002600-43002800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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

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