Variant report

Variant	rs1010576
Chromosome Location	chr14:82072476-82072477
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]
rs10131684	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12436893	0.92[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12587847	0.82[JPT][hapmap]
rs12588582	0.96[ASN][1000 genomes]
rs1957535	0.98[ASN][1000 genomes]
rs1957538	0.87[EUR][1000 genomes]
rs4464014	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4904007	0.87[EUR][1000 genomes]
rs4904008	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4904013	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7140517	0.82[JPT][hapmap]
rs7147672	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7157873	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7161117	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8006683	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8007709	0.95[CEU][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8017982	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs932666	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]

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	nsv1047694	chr14:81831147-82534026	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv542145	chr14:81831147-82534026	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv565299	chr14:81983027-82586324	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1052666	chr14:82069162-83028382	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1010576	SPTLC2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:82068000-82076400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr14:82072200-82073000	Enhancers	Fetal Stomach	stomach

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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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