Variant report

Variant	rs6425400
Chromosome Location	chr1:171718833-171718834
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	chr1:171716243..171719064-chr1:171724959..171726661,2	K562	blood:

Variant related genes	Relation type
ENSG00000271459	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10798598	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10798599	1.00[CEU][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes]
rs10798603	1.00[CEU][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10913508	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10913530	1.00[CEU][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10913559	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10913578	0.81[YRI][hapmap]
rs10913586	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11583530	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11805692	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11806314	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12045452	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12096984	1.00[CEU][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12120152	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12139610	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2073484	1.00[CEU][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2227229	1.00[CEU][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3753539	0.81[YRI][hapmap]
rs4342884	1.00[CEU][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4468194	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6662836	0.95[CEU][hapmap];0.83[JPT][hapmap]
rs6665581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668623	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6672082	1.00[CEU][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6673782	1.00[CEU][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6674468	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6674688	1.00[CEU][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6674774	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6682452	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6685742	0.89[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6688447	1.00[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6700606	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap]
rs763225	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9659578	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs9943293	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs999685	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6425400	VAMP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171712000-171723400	Weak transcription	Lung	lung
2	chr1:171713600-171722200	Weak transcription	NHLF	lung
3	chr1:171713600-171722800	Weak transcription	HMEC	breast
4	chr1:171715600-171720000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr1:171715800-171719800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr1:171718600-171723000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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