Variant report

Variant	rs10739978
Chromosome Location	chr9:93152717-93152718
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10739975	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1365368	0.81[ASN][1000 genomes]
rs1426506	0.82[ASN][1000 genomes]
rs1648474	0.81[ASN][1000 genomes]
rs1777014	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1777034	0.81[ASN][1000 genomes]
rs1777052	0.83[ASN][1000 genomes]
rs1946378	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2114345	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2114346	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2798041	0.82[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6479556	0.82[ASN][1000 genomes]
rs6479594	0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs6479602	0.88[CEU][hapmap];0.92[CHB][hapmap]
rs7037348	0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap]
rs890427	0.89[CEU][hapmap];0.92[CHB][hapmap]
rs981129	0.89[CEU][hapmap];0.92[CHB][hapmap]
rs992224	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041278	chr9:92965701-93560454	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv528155	chr9:93106543-93152717	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv482748	chr9:93123377-93279526	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv893565	chr9:93130796-93392332	Genic enhancers Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10739978	SPTLC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93147400-93156000	Weak transcription	H1 Derived Mesenchymal Stem 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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