Variant report

Variant	rs6662126
Chromosome Location	chr1:171643268-171643269
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171642979..171645264-chr1:171671539..171674041,2	MCF-7	breast:
2	chr1:171642202..171644426-chr1:171645702..171648061,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10157798	0.92[ASN][1000 genomes]
rs10489248	0.94[ASN][1000 genomes]
rs10913408	0.92[ASN][1000 genomes]
rs10913455	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913457	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913458	0.94[ASN][1000 genomes]
rs11799938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11799961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800109	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11800328	0.81[ASN][1000 genomes]
rs11800358	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11801283	0.81[ASN][1000 genomes]
rs11801712	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11802265	0.82[ASN][1000 genomes]
rs11809518	0.97[ASN][1000 genomes]
rs11809796	0.97[ASN][1000 genomes]
rs11811408	0.97[ASN][1000 genomes]
rs11811876	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12063563	0.81[ASN][1000 genomes]
rs12145527	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12145593	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16864740	0.97[ASN][1000 genomes]
rs1894664	0.97[ASN][1000 genomes]
rs2014613	0.94[ASN][1000 genomes]
rs34324629	0.84[ASN][1000 genomes]
rs56941416	0.97[ASN][1000 genomes]
rs56994188	0.97[ASN][1000 genomes]
rs57689480	0.97[ASN][1000 genomes]
rs58035845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59146152	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs60554980	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684567	0.92[ASN][1000 genomes]
rs6703259	0.87[ASN][1000 genomes]
rs73041958	0.97[ASN][1000 genomes]
rs73041960	0.97[ASN][1000 genomes]
rs73041965	0.97[ASN][1000 genomes]
rs73041966	0.97[ASN][1000 genomes]
rs73041973	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7536328	0.97[ASN][1000 genomes]
rs7541132	0.97[ASN][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
rs6662126	VAMP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171637000-171643800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:171643200-171643600	Weak transcription	Fetal Stomach	stomach
3	chr1:171643200-171645000	Enhancers	Rectal Smooth Muscle	rectum

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