Variant report

Variant	rs62297622
Chromosome Location	chr4:80563489-80563490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1866835	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2582681	0.86[AMR][1000 genomes]
rs2709847	0.86[AMR][1000 genomes]
rs3109166	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3111790	0.90[ASN][1000 genomes]
rs60613746	0.91[ASN][1000 genomes]
rs62297619	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62297620	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7665378	0.93[ASN][1000 genomes]
rs7687586	0.92[ASN][1000 genomes]
rs7688923	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7697040	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs894054	0.86[AMR][1000 genomes]
rs894055	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879506	chr4:80316417-80604625	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1002031	chr4:80459528-80759113	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1005152	chr4:80549659-80814456	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62297622	LINC00989	cis	Skin Sun Exposed Lower leg	GTEx
rs62297622	LINC00989	cis	Whole Blood	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:80555600-80566600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:80555600-80566800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr4:80559600-80566600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr4:80563200-80566600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:80563400-80563600	Enhancers	hESC Derived CD184+ Endoderm Cultured 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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