Variant report

Variant	rs6667559
Chromosome Location	chr1:171653957-171653958
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr1:171653943-171653957	K562	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VAMP4-4	chr1:171653555-171654384	NONHSAT007576
2	lnc-VAMP4-4	chr1:171653836-171654384	NONHSAT007577
3	lnc-VAMP4-4	chr1:171653921-171654384	l_147_chr1:171653920-171677715_76bGuttman_hLF

Variant related genes	Relation type
RPL4P3	TF binding region

Extended variants
information (count: 78 )
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]
rs11576221	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]
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]
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:5 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6667559	VAMP4	cis	Frontal Cortex	GTEx
rs6667559	METTL13	cis	parietal	SCAN
rs6667559	VAMP4	cis	multi-tissue	Pritchard
rs6667559	VAMP4	cis	Temporal Cortex	GTEx
rs6667559	VAMP4	cis	Cerebellum	GTEx
rs6667559	VAMP4	cis	Brain Pons	GTEx
rs6667559	VAMP4	cis	lymphoblastoid	seeQTL
rs6667559	PRDX6	cis	parietal	SCAN

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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