Variant report

Variant	rs62010552
Chromosome Location	chr15:78987686-78987687
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1114829	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11633519	0.81[EUR][1000 genomes]
rs12907511	0.85[EUR][1000 genomes]
rs1809415	0.82[EUR][1000 genomes]
rs28661610	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2869552	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58717592	0.83[EUR][1000 genomes]
rs62010554	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6495317	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6495318	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7163236	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7170552	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7170563	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72625802	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8039600	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]

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	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv1045827	chr15:78907656-79004642	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv457208	chr15:78908032-79019610	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv570201	chr15:78908032-79019610	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv974713	chr15:78945824-78996783	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62010552	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs62010552	CHRNA5	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78979000-78988400	Weak transcription	Left Ventricle	heart
2	chr15:78983600-78988800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr15:78984000-78988200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr15:78984600-78988200	Weak transcription	Esophagus	oesophagus
5	chr15:78984800-78988200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:78986600-78988600	Enhancers	Spleen	Spleen
7	chr15:78987000-78988000	Weak transcription	Liver	Liver
8	chr15:78987400-78988600	Enhancers	GM12878-XiMat	blood

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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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