Variant report

Variant	rs1430785
Chromosome Location	chr2:67869292-67869293
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1023691	0.87[EUR][1000 genomes]
rs1023693	0.87[EUR][1000 genomes]
rs1430789	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1430790	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1430791	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1430792	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2861684	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2861698	0.94[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs2861700	0.94[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs2861701	0.94[CEU][hapmap]
rs2902024	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4533457	0.94[CEU][hapmap]
rs4671817	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7569813	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7595894	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9309402	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs980227	0.81[AMR][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	nsv534389	chr2:67388428-68225338	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1430785	VAX2	cis	parietal	SCAN
rs1430785	NAGK	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:67866800-67884200	Weak transcription	Aorta	Aorta
2	chr2:67867200-67872400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr2:67867200-67872600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr2:67869200-67869400	Enhancers	Pancreas	Pancrea
5	chr2:67869200-67869600	Enhancers	Fetal Kidney	kidney
6	chr2:67869200-67869600	Flanking Active TSS	Hela-S3	cervix
7	chr2:67869200-67871200	Enhancers	Fetal Lung	lung

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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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