Variant report

Variant	rs2487742
Chromosome Location	chr1:179727752-179727753
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10913881	1.00[CHD][hapmap]
rs2454199	0.85[MEX][hapmap]
rs2487741	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2487743	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2504044	0.92[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2504045	0.91[CEU][hapmap]
rs2504046	0.84[CEU][hapmap]
rs2504047	0.86[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][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	nsv1009961	chr1:179714247-179790110	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2487742	PAPPA2	cis	parietal	SCAN
rs2487742	MRPS14	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179727000-179727800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:179727600-179727800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:179727600-179728000	Enhancers	hESC Derived CD56+ Mesoderm Cultured 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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