Variant report

Variant	rs6659539
Chromosome Location	chr1:171653867-171653868
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VAMP4-4	chr1:171653555-171654384	NONHSAT007576
2	lnc-VAMP4-4	chr1:171653836-171654384	NONHSAT007577

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10798598	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10798599	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10798603	0.82[EUR][1000 genomes]
rs10913488	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10913508	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10913530	0.82[EUR][1000 genomes]
rs10913559	0.82[EUR][1000 genomes]
rs11583530	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11805692	0.81[EUR][1000 genomes]
rs11806314	0.82[EUR][1000 genomes]
rs12045452	0.81[EUR][1000 genomes]
rs12096984	0.82[EUR][1000 genomes]
rs12139610	0.82[EUR][1000 genomes]
rs2073484	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2227229	0.82[EUR][1000 genomes]
rs4342884	0.80[EUR][1000 genomes]
rs4468194	0.82[EUR][1000 genomes]
rs6668623	0.82[EUR][1000 genomes]
rs6672082	0.82[EUR][1000 genomes]
rs6673782	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6674468	0.81[EUR][1000 genomes]
rs6674688	0.81[EUR][1000 genomes]
rs6674774	0.81[EUR][1000 genomes]
rs6682452	0.81[EUR][1000 genomes]
rs6685742	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6688447	0.82[EUR][1000 genomes]
rs763225	0.82[EUR][1000 genomes]
rs9660076	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs999685	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers 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	23 gene(s)	inside rSNPs	diseases
5	nsv872544	chr1:171616822-171654968	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6659539	VAMP4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171653000-171654200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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