Variant report

Variant	rs40468
Chromosome Location	chr5:4982814-4982815
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10038746	0.92[EUR][1000 genomes]
rs10038747	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10058490	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1035914	0.92[EUR][1000 genomes]
rs1452027	0.92[EUR][1000 genomes]
rs168733	0.87[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs181822	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs189835	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1901498	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2399756	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs249457	0.90[EUR][1000 genomes]
rs249458	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs249459	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2561719	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2561720	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs2561721	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs2561722	0.92[EUR][1000 genomes]
rs2600655	0.84[EUR][1000 genomes]
rs30449	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs30450	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs30451	0.87[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs30462	0.90[EUR][1000 genomes]
rs30463	0.92[EUR][1000 genomes]
rs30464	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs30465	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs30466	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs30468	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs30469	0.90[EUR][1000 genomes]
rs30470	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs30471	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs30472	0.91[EUR][1000 genomes]
rs30473	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs30474	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs30475	0.92[EUR][1000 genomes]
rs374207	0.91[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs39586	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39849	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs39850	0.92[EUR][1000 genomes]
rs39851	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs39852	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs39853	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42400	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42401	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42545	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42546	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60185285	0.92[EUR][1000 genomes]
rs719183	0.96[EUR][1000 genomes]
rs9313095	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs935857	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs935858	0.92[EUR][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	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	esv2757980	chr5:4980876-5184615	Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	esv2759318	chr5:4980876-5184615	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1024784	chr5:4980979-5391231	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv880436	chr5:4982643-5038540	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs40468	LAMP3	trans	cerebellum	SCAN
rs40468	TERT	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:4982800-4983800	Enhancers	Fetal Kidney	kidney
2	chr5:4982800-4984400	Enhancers	Ovary	ovary

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