Variant report

Variant	rs254616
Chromosome Location	chr5:52446197-52446198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITGA2-3	chr5:52445214-52446721	l_2918_chr5:52441399-52446721_testes

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1374057	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs152945	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs194218	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs251331	0.82[JPT][hapmap]
rs251332	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs254596	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs254606	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs254607	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs254608	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs254609	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs254611	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs254613	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs254615	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs254626	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2547521	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2547523	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2652545	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs30087	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs30089	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs30090	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs30091	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs30095	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs30096	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs30097	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs30714	0.83[CHB][hapmap]
rs34781824	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs376850	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs390421	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs402741	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs448453	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7710432	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv980563	chr5:52436848-52446366	Inactive region	lncRNA	n/a	inside rSNPs	diseases

No data

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

No data

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