Variant report

Variant	rs4964462
Chromosome Location	chr12:104423570-104423571
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1038497	0.88[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.95[ASN][1000 genomes]
rs11111876	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12820602	1.00[ASW][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs2583228	0.91[ASN][1000 genomes]
rs4135128	0.90[MKK][hapmap]

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	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv973113	chr12:104421941-104426122	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4964462	APAF1	cis	cerebellum	SCAN
rs4964462	GLT8D2	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104408800-104428000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:104408800-104442200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:104415200-104435200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:104420000-104435200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:104421200-104435200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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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

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