Variant report

Variant	rs17649250
Chromosome Location	chr1:171720586-171720587
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1001373	1.00[CEU][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10489249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052676	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10753181	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10903	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10913489	0.80[EUR][1000 genomes]
rs10913490	0.80[EUR][1000 genomes]
rs10913492	0.80[EUR][1000 genomes]
rs10913511	0.92[EUR][1000 genomes]
rs10913514	0.92[EUR][1000 genomes]
rs10913529	1.00[CEU][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10913565	1.00[CEU][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10913578	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913582	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[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]
rs10913587	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913625	0.85[YRI][hapmap]
rs11576221	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs11577073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577197	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577745	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578179	0.92[EUR][1000 genomes]
rs11578699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579698	0.93[EUR][1000 genomes]
rs11580415	0.93[EUR][1000 genomes]
rs11580522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11583920	1.00[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11590680	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590714	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11799420	0.80[EUR][1000 genomes]
rs11801846	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11803174	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11808099	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11811780	0.81[EUR][1000 genomes]
rs12119232	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12123727	0.83[EUR][1000 genomes]
rs12126566	0.91[ASN][1000 genomes]
rs12127026	0.93[EUR][1000 genomes]
rs12128536	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12132221	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs15655	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16843230	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16843251	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17649050	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17649068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298914	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2421911	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3753539	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]
rs3766653	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55670848	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58455759	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6656003	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6659874	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6662720	1.00[CEU][hapmap]
rs6667559	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs6669263	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6670427	1.00[CEU][hapmap]
rs6678890	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6679027	0.81[YRI][hapmap]
rs6679354	0.93[EUR][1000 genomes]
rs6688823	0.85[YRI][hapmap]
rs7536436	0.93[EUR][1000 genomes]
rs7536543	0.93[EUR][1000 genomes]
rs9661596	0.80[EUR][1000 genomes]
rs9662506	1.00[CEU][hapmap]
rs9662853	0.80[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs17649250	VAMP4	cis	Brain Pons	GTEx
rs17649250	PRDX6	cis	parietal	SCAN
rs17649250	ANO3	trans	lymphoblastoid	seeQTL
rs17649250	MAEL	cis	cerebellum	SCAN
rs17649250	VAMP4	cis	Frontal Cortex	GTEx
rs17649250	VAMP4	cis	lymphoblastoid	seeQTL
rs17649250	VAMP4	cis	Temporal Cortex	GTEx
rs17649250	BCHE	trans	lymphoblastoid	seeQTL
rs17649250	VAMP4	cis	multi-tissue	Pritchard

Chromatin state (count:5 , 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	chr1:171718600-171723000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:171720000-171721200	Enhancers	Monocytes-CD14+_RO01746	blood

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