Variant report

Variant	rs34890793
Chromosome Location	chr3:49619493-49619494
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 20 )

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

rs_ID	r²[population]
rs1009051	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs10452032	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap]
rs1078341	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap]
rs10865956	1.00[CHD][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap]
rs11130207	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11130208	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11130211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11130217	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap]
rs11709734	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs11720705	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs11721148	0.80[AMR][1000 genomes]
rs11928090	1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs12583	1.00[CHD][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap]
rs12637313	0.94[CEU][hapmap];1.00[CHD][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12715437	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap]
rs13096474	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs13096480	0.80[AMR][1000 genomes]
rs13322887	1.00[CHD][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap]
rs1352889	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.80[AMR][1000 genomes]
rs1463728	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1464569	0.93[ASW][hapmap];1.00[CHB][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap]
rs1491983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1491985	0.94[CEU][hapmap]
rs1532204	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1586827	0.94[CEU][hapmap];0.80[AMR][1000 genomes]
rs1982861	1.00[CHD][hapmap];0.80[LWK][hapmap];0.92[MKK][hapmap]
rs2029591	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2131108	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.80[AMR][1000 genomes]
rs2140270	1.00[CHD][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap]
rs2312462	1.00[CHD][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap]
rs2329021	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap]
rs2329025	0.81[AFR][1000 genomes]
rs3020779	0.93[CEU][hapmap]
rs3866330	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs3870339	0.87[AFR][1000 genomes]
rs3870341	0.91[AFR][1000 genomes]
rs3905330	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs4241405	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4241407	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap]
rs4855833	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.80[AMR][1000 genomes]
rs4855845	0.94[CEU][hapmap]
rs4855846	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap]
rs4855848	0.82[AMR][1000 genomes]
rs4855849	0.80[AMR][1000 genomes]
rs4855858	0.87[AFR][1000 genomes]
rs4855882	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs4855885	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs6446284	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446285	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6774202	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap]
rs6797299	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6805609	1.00[CHD][hapmap]
rs7374731	0.83[AFR][1000 genomes]
rs7613603	0.94[CEU][hapmap]
rs7622786	0.86[AFR][1000 genomes]
rs7625857	0.94[AFR][1000 genomes]
rs7628207	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap]
rs7644148	1.00[CHD][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap]
rs7653505	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs8897	1.00[CHD][hapmap]
rs940045	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs9809237	0.85[AFR][1000 genomes]
rs9824435	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs9829155	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap]
rs9830730	0.94[CEU][hapmap]
rs9835157	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap]
rs9849038	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs9860055	1.00[CHD][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap]
rs9862534	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes]
rs9870755	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap]
rs9870858	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs9871024	1.00[CHD][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap]
rs9883000	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs34890793	ZNF589	cis	parietal	SCAN
rs34890793	DALRD3	cis	cerebellum	SCAN
rs34890793	NME6	cis	cerebellum	SCAN
rs34890793	AMT	cis	cerebellum	SCAN
rs34890793	AMT	cis	parietal	SCAN
rs34890793	WDR6	cis	Muscle Skeletal	GTEx
rs34890793	WDR6	cis	cerebellum	SCAN
rs34890793	DALRD3	cis	parietal	SCAN
rs34890793	AMT	cis	Thyroid	GTEx
rs34890793	ARIH2	cis	cerebellum	SCAN
rs34890793	LZTFL1	cis	cerebellum	SCAN
rs34890793	NICN1	cis	Thyroid	GTEx
rs34890793	QRICH1	cis	cerebellum	SCAN
rs34890793	GNL3	cis	cerebellum	SCAN
rs34890793	GMPPB	cis	parietal	SCAN
rs34890793	RNF123	cis	parietal	SCAN
rs34890793	AMT	cis	Whole Blood	GTEx
rs34890793	AMT	cis	lung	GTEx
rs34890793	NICN1-AS1	cis	Thyroid	GTEx
rs34890793	P4HTM	cis	parietal	SCAN

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
chromosomal regions: chr1:12345-34567

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