Variant report

Variant	rs2440341
Chromosome Location	chr15:53170722-53170723
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1899740	0.85[AMR][1000 genomes]
rs2068106	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2120446	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2414188	0.85[AMR][1000 genomes]
rs2440328	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2440343	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4776080	0.81[MEX][hapmap];0.83[AMR][1000 genomes]
rs7177989	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1043999	chr15:53162917-53187508	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2440341	SCG3	cis	parietal	SCAN
rs2440341	EID1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53165800-53183200	Weak transcription	Pancreas	Pancrea
2	chr15:53168000-53172800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:53168400-53172200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:53170600-53171200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:53170600-53172400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:53170600-53172600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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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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