Variant report

Variant	rs2174696
Chromosome Location	chr1:165283470-165283471
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 5 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11807536	0.83[CEU][hapmap]
rs1807798	0.81[JPT][hapmap]
rs7534017	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7540476	0.96[CEU][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap];0.84[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	nsv869712	chr1:164866810-165299085	Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2174696	LRRC52	cis	cerebellum	SCAN
rs2174696	B4GALT3	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165283000-165283800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:165283200-165283600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:165283200-165283600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:165283400-165283800	Enhancers	hESC Derived CD56+ Ectoderm 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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