Variant report

Variant	rs2999504
Chromosome Location	chr1:216905611-216905612
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10863269	0.82[CHD][hapmap]
rs11117669	0.83[CHD][hapmap]
rs12059942	0.93[EUR][1000 genomes]
rs12070175	0.87[CHD][hapmap]
rs1339350	1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1339357	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17043393	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs17043570	0.91[CHD][hapmap];0.87[GIH][hapmap]
rs2789730	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2789732	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2789733	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2820875	0.86[ASN][1000 genomes]
rs2820876	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2820878	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv508694	chr1:216901014-216923883	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2999504	SMYD2	cis	cerebellum	SCAN
rs2999504	C1orf97	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216897400-216958600	Weak transcription	Pancreas	Pancrea
2	chr1:216905200-216909800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:216905200-216913200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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