Variant report

Variant	rs874977
Chromosome Location	chr9:93111241-93111242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10761373	0.81[JPT][hapmap]
rs10821444	0.82[JPT][hapmap]
rs10821452	0.80[JPT][hapmap]
rs10993468	0.81[JPT][hapmap]
rs10993469	0.81[JPT][hapmap]
rs1418936	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1581933	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1754093	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1777035	0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2771080	0.83[CEU][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2771081	0.83[CEU][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2798038	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2798051	0.80[ASN][1000 genomes]
rs3748185	0.82[JPT][hapmap]
rs3748186	0.82[JPT][hapmap]
rs3748187	0.82[JPT][hapmap]
rs6479595	0.82[JPT][hapmap]
rs7870764	0.82[JPT][hapmap]
rs9332454	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051180	chr9:92869383-93141038	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv540169	chr9:92869383-93141038	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	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
4	nsv893564	chr9:93074228-93116944	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs874977	SPTLC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93103000-93111400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:93106400-93111800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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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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