Variant report

Variant	rs10500580
Chromosome Location	chr16:73950557-73950558
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10500579	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12051084	0.92[EUR][1000 genomes]
rs12051297	0.88[EUR][1000 genomes]
rs12597453	0.87[EUR][1000 genomes]
rs2526075	0.84[EUR][1000 genomes]
rs2663156	0.85[EUR][1000 genomes]
rs2663157	0.82[EUR][1000 genomes]
rs4888052	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs67456789	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9927723	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906900	chr16:73650853-74349043	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv457519	chr16:73664748-74041721	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv572969	chr16:73664748-74041721	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv906901	chr16:73752982-74455293	Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv833275	chr16:73840999-74043712	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv525758	chr16:73899352-74052556	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10500580	C7orf62	trans	parietal	SCAN
rs10500580	WDR59	cis	parietal	SCAN
rs10500580	TMCO7	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:73945600-73951600	Enhancers	Fetal Brain Male	brain
2	chr16:73947000-73950800	Weak transcription	Fetal Lung	lung
3	chr16:73949000-73951200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:73949200-73950600	Enhancers	H1 Cell Line	embryonic stem cell
5	chr16:73949600-73951200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr16:73949600-73951400	Enhancers	Fetal Brain Female	brain
7	chr16:73950000-73950800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr16:73950000-73951000	Weak transcription	Brain Germinal Matrix	brain
9	chr16:73950000-73951400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr16:73950200-73951400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr16:73950400-73951400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr16:73950400-73952400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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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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