Variant report

Variant	rs1452027
Chromosome Location	chr5:4968029-4968030
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MED10-10	chr5:4967877-4968116	ENSG00000251506

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10038746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10038747	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10058490	0.81[EUR][1000 genomes]
rs1035914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168733	0.81[EUR][1000 genomes]
rs181822	0.83[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs189835	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1901498	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2399756	0.82[EUR][1000 genomes]
rs249457	0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs249458	0.81[EUR][1000 genomes]
rs249459	0.81[EUR][1000 genomes]
rs2561719	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2561720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2561721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2561722	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2600655	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs30449	0.81[EUR][1000 genomes]
rs30450	0.83[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs30451	0.81[EUR][1000 genomes]
rs30462	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs30463	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs30464	0.83[EUR][1000 genomes]
rs30465	0.83[EUR][1000 genomes]
rs30466	0.83[EUR][1000 genomes]
rs30468	0.83[EUR][1000 genomes]
rs30469	0.83[EUR][1000 genomes]
rs30470	0.86[EUR][1000 genomes]
rs30471	0.86[EUR][1000 genomes]
rs30472	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30473	0.92[EUR][1000 genomes]
rs30474	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs30475	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs374207	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39586	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs39849	0.83[EUR][1000 genomes]
rs39850	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs39851	0.83[EUR][1000 genomes]
rs39852	0.83[EUR][1000 genomes]
rs39853	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs40468	0.92[EUR][1000 genomes]
rs42400	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs42401	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs42545	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs42546	0.97[EUR][1000 genomes]
rs60185285	0.84[EUR][1000 genomes]
rs719183	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9313095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019579	chr5:4557477-4997411	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1021653	chr5:4932992-5201887	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1028717	chr5:4954566-4993583	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2588778	chr5:4968027-4968029	Inactive region	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1452027	TERT	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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