Variant report

Variant	rs3753539
Chromosome Location	chr1:171716185-171716186
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr1:171716168-171716191	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:171715474..171717063-chr1:171747141..171749342,2	K562	blood:
2	chr1:171711002..171712859-chr1:171714467..171716511,2	MCF-7	breast:
3	chr1:171715364..171718014-chr1:171745246..171747698,2	MCF-7	breast:
4	chr1:171705072..171707837-chr1:171716105..171717838,2	K562	blood:
5	chr1:171714902..171716862-chr1:171721473..171724148,2	K562	blood:

No data

Variant related genes	Relation type
VAMP4	TF binding region
ENSG00000117533	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1001373	0.88[GIH][hapmap];0.83[JPT][hapmap]
rs10489249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10489251	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10753181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798603	0.82[GIH][hapmap];0.82[YRI][hapmap]
rs10913507	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10913529	0.88[GIH][hapmap];0.83[JPT][hapmap]
rs10913530	0.83[GIH][hapmap];0.82[YRI][hapmap]
rs10913565	0.83[JPT][hapmap]
rs10913578	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913582	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913587	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11576221	0.84[GIH][hapmap]
rs11577073	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11577197	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11577745	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11578699	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11578723	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11580522	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11583920	0.83[JPT][hapmap]
rs11590680	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11590714	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12096984	0.86[YRI][hapmap]
rs12119232	0.94[ASN][1000 genomes]
rs12120152	0.89[YRI][hapmap]
rs12126566	0.90[ASN][1000 genomes]
rs15655	0.88[GIH][hapmap]
rs16843230	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16843251	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17649050	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17649068	0.99[ASN][1000 genomes]
rs17649250	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs2073484	0.83[GIH][hapmap];0.89[YRI][hapmap]
rs2227229	0.86[YRI][hapmap]
rs2298914	0.81[GIH][hapmap];0.83[JPT][hapmap]
rs2421911	0.90[ASN][1000 genomes]
rs4342884	0.83[GIH][hapmap]
rs4468194	0.82[YRI][hapmap]
rs6665581	0.89[YRI][hapmap]
rs6667559	0.84[GIH][hapmap]
rs6670427	0.83[CEU][hapmap]
rs6672082	0.85[YRI][hapmap]
rs6673782	0.89[YRI][hapmap]
rs6674688	0.83[GIH][hapmap];0.86[YRI][hapmap]
rs6685742	0.83[GIH][hapmap]
rs6700606	0.82[YRI][hapmap]
rs999685	0.82[YRI][hapmap]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3753539	VAMP4	Cis_1M	lymphoblastoid	RTeQTL
rs3753539	METTL13	cis	parietal	SCAN
rs3753539	VAMP4	cis	Frontal Cortex	GTEx
rs3753539	DNM3	cis	cerebellum	SCAN
rs3753539	VAMP4	cis	multi-tissue	Pritchard
rs3753539	VAMP4	cis	Brain Pons	GTEx
rs3753539	VAMP4	cis	lymphoblastoid	seeQTL
rs3753539	DCAF6	cis	cerebellum	SCAN

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	chr1:171713400-171716200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:171713600-171722200	Weak transcription	NHLF	lung
4	chr1:171713600-171722800	Weak transcription	HMEC	breast
5	chr1:171715600-171720000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr1:171715800-171719800	Weak transcription	Primary monocytes fromperipheralblood	blood

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