Variant report

Variant	rs11576221
Chromosome Location	chr1:171653696-171653697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VAMP4-4	chr1:171653555-171654384	NONHSAT007576

Extended variants
information (count: 79 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1001373	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10157798	0.82[CHD][hapmap]
rs10489249	1.00[CEU][hapmap]
rs10489251	0.80[EUR][1000 genomes]
rs1052676	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10903	0.86[EUR][1000 genomes]
rs10913475	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10913489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913492	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913511	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10913514	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10913529	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10913565	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10913578	0.85[GIH][hapmap]
rs10913582	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs10913587	0.80[EUR][1000 genomes]
rs11577073	0.80[EUR][1000 genomes]
rs11577197	0.80[EUR][1000 genomes]
rs11577745	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs11578179	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11578699	0.80[EUR][1000 genomes]
rs11578723	0.80[EUR][1000 genomes]
rs11579698	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11580415	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11580522	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs11583920	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11590680	0.80[EUR][1000 genomes]
rs11590714	0.80[EUR][1000 genomes]
rs11799420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11799938	0.86[CHD][hapmap]
rs11799961	0.84[CHD][hapmap]
rs11801846	0.85[EUR][1000 genomes]
rs11802265	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11803174	0.85[EUR][1000 genomes]
rs11808099	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11811780	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118409	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12119232	0.82[EUR][1000 genomes]
rs12119553	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12123727	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12125429	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12127026	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12128536	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12132221	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs15655	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs17649050	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs17649250	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs2298914	1.00[CEU][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs3753539	0.84[GIH][hapmap]
rs3766653	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55670848	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56091821	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56345529	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58455759	0.85[EUR][1000 genomes]
rs6656003	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6659874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs6662720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6667559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[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]
rs6669263	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6670427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6678890	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6679354	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6687922	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6688018	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7528057	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7536436	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7536543	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9659845	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9661596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9662174	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9662506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9662853	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv946504	chr1:171652643-171653781	Enhancers Weak transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11576221	PRDX6	cis	parietal	SCAN
rs11576221	VAMP4	Cis_1M	lymphoblastoid	RTeQTL
rs11576221	VAMP4	cis	lymphoblastoid	seeQTL
rs11576221	VAMP4	cis	Brain Pons	GTEx
rs11576221	VAMP4	cis	multi-tissue	Pritchard
rs11576221	METTL13	cis	parietal	SCAN
rs11576221	VAMP4	cis	Frontal Cortex	GTEx
rs11576221	VAMP4	cis	Temporal Cortex	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171653000-171654200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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