Variant report

Variant	rs2805840
Chromosome Location	chr9:100505546-100505547
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NCBP1-1	chr9:100505490-100507217	ENSG00000260677.1
2	lnc-NCBP1-1	chr9:100505490-100505852	NONHSAT133532

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10983030	0.93[CEU][hapmap]
rs10983447	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12378130	0.80[ASN][1000 genomes]
rs12379552	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1800975	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2026132	0.92[CEU][hapmap]
rs2036959	0.92[CEU][hapmap];0.96[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2668792	1.00[CEU][hapmap];0.96[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2668793	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2668798	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2773347	0.92[CEU][hapmap]
rs2773351	0.93[CEU][hapmap]
rs2805767	0.92[CEU][hapmap]
rs2805777	0.92[CEU][hapmap]
rs2805779	0.88[CEU][hapmap]
rs2805824	1.00[CEU][hapmap];0.96[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2805825	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2805826	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2805828	0.92[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2805829	0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2805832	0.87[EUR][1000 genomes]
rs2805837	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2805839	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2808668	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs2808673	0.92[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2808675	0.92[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2808677	0.93[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2808683	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808685	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808686	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808687	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808689	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808691	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808692	0.95[EUR][1000 genomes]
rs2808694	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808701	1.00[EUR][1000 genomes]
rs2808703	0.87[EUR][1000 genomes]
rs7465737	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs958346	0.89[CEU][hapmap]

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	nsv1043753	chr9:100458109-100599265	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv614934	chr9:100482976-100550253	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100504000-100514000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:100505400-100509600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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