Variant report

Variant	rs2569489
Chromosome Location	chr19:51584743-51584744
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10445581	0.81[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10500304	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16988866	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs17658926	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1880416	0.93[ASN][1000 genomes]
rs2569488	0.84[ASN][1000 genomes]
rs2569491	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs35287116	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6509518	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7351079	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs9304708	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34104	chr19:51566170-51641675	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2569489	ZNF587	cis	cerebellum	SCAN
rs2569489	ZNF415	cis	cerebellum	SCAN
rs2569489	EPN1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51580000-51587800	Weak transcription	Right Atrium	heart
2	chr19:51580600-51586200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr19:51583000-51589600	Weak transcription	Spleen	Spleen
4	chr19:51583000-51604200	Weak transcription	Left Ventricle	heart
5	chr19:51583200-51585800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:51583200-51586400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr19:51583200-51589000	Weak transcription	Pancreas	Pancrea
8	chr19:51583200-51589600	Weak transcription	Esophagus	oesophagus
9	chr19:51583200-51595400	Weak transcription	Gastric	stomach
10	chr19:51583200-51597000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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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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