Variant report

Variant	rs2958468
Chromosome Location	chr17:20728897-20728898
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDRT15L2-6	chr17:20728896-20731392	NONHSAT146837

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11653352	0.87[ASN][1000 genomes]
rs11653660	0.97[ASN][1000 genomes]
rs1815568	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1815572	0.97[ASN][1000 genomes]
rs1856276	0.98[ASN][1000 genomes]
rs1974277	0.87[ASN][1000 genomes]
rs1974279	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1999864	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28538692	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2958466	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2958469	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2958479	0.93[ASN][1000 genomes]
rs2993351	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2993352	0.92[ASN][1000 genomes]
rs2993353	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2993360	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2993361	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2993369	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2993370	0.89[ASN][1000 genomes]
rs34695039	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35847073	0.89[ASN][1000 genomes]
rs4359505	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4508469	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4517848	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4520891	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4985929	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57273270	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60623070	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6587090	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7207243	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7220472	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7221311	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7222405	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7223908	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73298018	0.91[ASN][1000 genomes]
rs73982310	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8079974	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9891333	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9893692	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9905676	0.93[ASN][1000 genomes]
rs9906238	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9906250	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9906720	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916440	chr17:20171468-20839266	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv2751619	chr17:20462908-20914156	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv3361931	chr17:20539962-20845258	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv469647	chr17:20552253-20751738	Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv482489	chr17:20552253-20751738	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	esv3330516	chr17:20572433-20862663	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv962442	chr17:20720727-20729310	Weak transcription ZNF genes & repeats Enhancers	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	chr17:20727800-20729200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr17:20728200-20729600	Enhancers	HepG2	liver
3	chr17:20728400-20729000	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr17:20728600-20729000	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links