Variant report

Variant	rs2662269
Chromosome Location	chr5:98076517-98076518
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11242487	0.85[ASN][1000 genomes]
rs12652843	0.85[ASN][1000 genomes]
rs12656672	0.85[ASN][1000 genomes]
rs2277929	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2545674	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545689	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2547963	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2547969	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3849789	0.85[ASN][1000 genomes]
rs3849790	0.85[ASN][1000 genomes]
rs60106201	0.85[ASN][1000 genomes]
rs61202875	0.81[ASN][1000 genomes]
rs72773668	0.85[ASN][1000 genomes]
rs72773670	0.85[ASN][1000 genomes]
rs992591	0.91[AMR][1000 genomes];0.99[EUR][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	nsv1032060	chr5:98022226-98093492	Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv537817	chr5:98022226-98093492	Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv882414	chr5:98063710-98193164	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2662269	RGMB	cis	normal skin	skin_eQTL
rs2662269	RGMB	Cis_1M	lymphoblastoid	RTeQTL
rs2662269	RGMB	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98070400-98076600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:98073400-98077800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:98073600-98077800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:98073600-98078200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:98076000-98077200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:98076200-98076800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr5:98076200-98077000	Enhancers	NHDF-Ad	bronchial
8	chr5:98076400-98077600	Weak transcription	Osteobl	bone

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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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