Variant report

Variant	rs9659578
Chromosome Location	chr1:171656124-171656125
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10798598	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10798599	0.81[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10798603	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs10913488	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10913508	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10913530	1.00[CEU][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs10913559	0.81[EUR][1000 genomes]
rs11805692	0.80[EUR][1000 genomes]
rs11806314	0.81[EUR][1000 genomes]
rs12045452	0.80[EUR][1000 genomes]
rs12096984	1.00[CEU][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs12120152	1.00[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs12139610	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2073484	1.00[CEU][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs2227229	1.00[CEU][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs4342884	1.00[CEU][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.97[TSI][hapmap]
rs4468194	1.00[CEU][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs6659539	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6662836	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6665581	1.00[CEU][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs6668623	0.81[EUR][1000 genomes]
rs6672082	1.00[CEU][hapmap];0.84[GIH][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs6673782	1.00[CEU][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs6674468	0.80[EUR][1000 genomes]
rs6674688	1.00[CEU][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes]
rs6674774	0.80[EUR][1000 genomes]
rs6682452	0.80[EUR][1000 genomes]
rs6685742	0.90[CEU][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6688447	1.00[CEU][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs6700606	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs763225	0.81[EUR][1000 genomes]
rs9660076	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9943293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs999685	1.00[CEU][hapmap];0.84[JPT][hapmap];0.81[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9659578	PRDX6	cis	parietal	SCAN
rs9659578	DNM3	cis	cerebellum	SCAN
rs9659578	VAMP4	cis	Brain Pons	GTEx
rs9659578	VAMP4	cis	multi-tissue	Pritchard
rs9659578	METTL13	cis	parietal	SCAN
rs9659578	VAMP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
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