Variant report

Variant	rs11578699
Chromosome Location	chr1:171719769-171719770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171719536..171721056-chr1:171729997..171731619,2	K562	blood:
2	chr1:171719571..171721308-chr1:171725110..171727162,2	MCF-7	breast:
3	chr1:171710699..171713555-chr1:171719677..171724483,6	MCF-7	breast:
4	chr1:171719352..171723049-chr1:171749265..171752646,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117533	Chromatin interaction
ENSG00000236741	Chromatin interaction
ENSG00000271459	Chromatin interaction
ENSG00000010165	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1001373	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10489249	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	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10913565	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10913578	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913582	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]
rs11576221	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	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578179	0.92[EUR][1000 genomes]
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	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11583920	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	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16843230	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16843251	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17649050	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	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	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	0.80[EUR][1000 genomes]
rs6667559	0.80[EUR][1000 genomes]
rs6669263	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6678890	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6679354	0.93[EUR][1000 genomes]
rs7536436	0.93[EUR][1000 genomes]
rs7536543	0.93[EUR][1000 genomes]
rs9661596	0.80[EUR][1000 genomes]
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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11578699	VAMP4	cis	multi-tissue	Pritchard
rs11578699	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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