Variant report

Variant	rs463020
Chromosome Location	chr20:15638912-15638913
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1420440	0.91[JPT][hapmap];0.93[MKK][hapmap];0.82[YRI][hapmap]
rs2023386	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2423968	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2423969	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs2423970	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs377187	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs448644	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs455659	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs459448	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs459928	0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs459989	0.91[JPT][hapmap]
rs460066	0.83[AFR][1000 genomes]
rs460654	0.91[JPT][hapmap];0.82[YRI][hapmap]
rs462849	0.90[JPT][hapmap]
rs464304	0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs464735	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs465416	0.88[CEU][hapmap]
rs465525	0.88[CEU][hapmap]
rs466243	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6131684	0.82[YRI][hapmap]
rs6135477	0.92[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs6135478	0.89[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6135480	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][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
rs463020	SPTLC3	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:15634000-15641200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:15635400-15639000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr20:15635600-15639000	Weak transcription	Brain Hippocampus Middle	brain
4	chr20:15637200-15639000	Weak transcription	Brain Substantia Nigra	brain
5	chr20:15637200-15640800	Weak transcription	NHDF-Ad	bronchial
6	chr20:15638800-15639600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr20:15638800-15640200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr20:15638800-15640600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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