Variant report

Variant	rs2616413
Chromosome Location	chr4:54598279-54598280
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GSX2-9	chr4:54596073-54598379	NONHSAT096406

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1382083	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2126715	0.84[EUR][1000 genomes]
rs2245157	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2590776	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2590790	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2590828	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2590830	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2590831	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2590832	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2616394	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2616397	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2616403	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2616406	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2616408	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2616414	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2898979	0.94[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs59445919	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62323723	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs728586	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73250987	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][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	esv15357	chr4:54591392-54603209	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv879015	chr4:54596466-54665559	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54584000-54600000	Weak transcription	Osteobl	bone
2	chr4:54597000-54599600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr4:54597000-54600200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:54597400-54598400	Weak transcription	NHDF-Ad	bronchial

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