Variant report

Variant	rs16840612
Chromosome Location	chr3:133412360-133412361
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11914965	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13061966	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13080154	0.95[JPT][hapmap]
rs13085923	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4420866	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4854592	0.90[EUR][1000 genomes]
rs4854593	0.90[EUR][1000 genomes]
rs4854742	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9283586	0.81[CHB][hapmap]
rs9985395	0.90[EUR][1000 genomes];0.81[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	nsv979783	chr3:133408825-133413260	Weak transcription Active TSS Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16840612	PRR23C	cis	parietal	SCAN
rs16840612	TOPBP1	cis	cerebellum	SCAN
rs16840612	SOX14	cis	parietal	SCAN
rs16840612	NEK11	cis	cerebellum	SCAN
rs16840612	TOPBP1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133411800-133430800	Weak transcription	Brain Angular Gyrus	brain
2	chr3:133412000-133415000	Enhancers	HepG2	liver
3	chr3:133412200-133437600	Weak transcription	Stomach Smooth Muscle	stomach

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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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