Variant report

Variant	rs465374
Chromosome Location	chr20:15644995-15644996
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1420433	0.89[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs416842	0.82[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs417099	0.82[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs455659	0.81[CEU][hapmap]
rs455709	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs456022	0.91[EUR][1000 genomes]
rs460411	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs460771	0.81[CEU][hapmap]
rs460818	0.89[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs465416	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs465525	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs465981	0.89[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6034249	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6034250	0.92[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs6043422	0.96[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs6135477	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869328	chr20:15325423-16213898	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2751909	chr20:15489871-15656007	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv833928	chr20:15619962-15780758	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs465374	SPTLC3	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:15642200-15645200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr20:15644200-15645200	Weak transcription	Ovary	ovary

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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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