Variant report

Variant	rs12958459
Chromosome Location	chr18:39915112-39915113
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIK3C3-5	chr18:39915049-39915268	ENSG00000267586.2
2	lnc-PIK3C3-5	chr18:39915049-39915268	NONHSAT059064
3	lnc-PIK3C3-5	chr18:39915049-39915268	NONHSAT059066
4	lnc-PIK3C3-5	chr18:39915049-39915268	ENSG00000267586.2
5	lnc-PIK3C3-5	chr18:39915049-39915268	ENSG00000267586.2

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

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

rs_ID	r²[population]
rs12958679	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16975918	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16975919	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16975921	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1841620	0.83[AMR][1000 genomes]
rs1841621	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1993752	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2085909	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2335780	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34642158	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34802524	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs391148	0.86[AMR][1000 genomes]
rs413718	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs414142	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs415805	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs415810	0.81[AMR][1000 genomes]
rs421436	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs428198	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs436343	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs449040	0.83[AMR][1000 genomes]
rs454565	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4621064	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66967065	0.89[ASN][1000 genomes]
rs68001532	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7232300	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7232594	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7235999	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7237280	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8085980	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8090017	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8096564	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs922266	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs976071	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9947788	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9947988	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9948169	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9959948	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9960132	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9964453	0.89[AMR][1000 genomes];0.89[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	nsv949609	chr18:39126941-40070286	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1059409	chr18:39711099-40139446	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39893200-39915200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr18:39910400-39916800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr18:39913800-39916600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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