Variant report

Variant	rs1856840
Chromosome Location	chr1:192811287-192811288
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10921278	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10921283	0.84[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap]
rs12404140	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1770915	0.83[LWK][hapmap]
rs1775686	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1775692	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1935824	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3900531	0.82[ASN][1000 genomes]
rs4140450	0.81[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap]
rs7534380	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7550636	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv548660	chr1:192609268-192945348	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1856840	RGS13	cis	parietal	SCAN
rs1856840	VPS53	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:192807200-192816000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:192809200-192812000	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr1:192810000-192816000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:192810600-192811400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr1:192810800-192811400	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr1:192811200-192812000	Enhancers	Aorta	Aorta

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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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