Variant report

Variant	rs16890459
Chromosome Location	chr5:59336110-59336111
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10037011	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10044529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10061543	0.95[EUR][1000 genomes]
rs10514886	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs10514887	0.92[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs10514902	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs11742066	0.85[EUR][1000 genomes]
rs11743973	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs11743977	0.90[EUR][1000 genomes]
rs11744029	0.90[EUR][1000 genomes]
rs11745357	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs11747070	0.90[EUR][1000 genomes]
rs11960746	0.89[EUR][1000 genomes]
rs12153039	0.92[CEU][hapmap]
rs12189373	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs12522367	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs13153508	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13157125	0.90[TSI][hapmap]
rs13160073	0.90[EUR][1000 genomes]
rs13175365	0.88[EUR][1000 genomes]
rs13177765	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs13177799	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs13179177	0.89[EUR][1000 genomes]
rs13184995	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13190681	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1369289	0.89[EUR][1000 genomes]
rs1396476	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs1508861	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1508863	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs1529842	0.81[EUR][1000 genomes]
rs1541961	0.81[EUR][1000 genomes]
rs1541962	0.85[EUR][1000 genomes]
rs16890451	0.86[ASW][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs16890455	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs16890516	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs16890521	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs16890523	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs17376533	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs17376568	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs17376761	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs17376788	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs17442232	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs17449821	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17449877	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17450114	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1836543	0.89[EUR][1000 genomes]
rs1876671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1946682	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2013733	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs2117551	0.86[CEU][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2662436	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs28388570	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2910835	0.85[EUR][1000 genomes]
rs2910836	0.85[EUR][1000 genomes]
rs2910837	0.85[EUR][1000 genomes]
rs2910839	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2916860	0.86[ASW][hapmap];0.93[CEU][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2961898	0.89[EUR][1000 genomes]
rs2961899	0.89[EUR][1000 genomes]
rs2961900	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs2962963	0.89[EUR][1000 genomes]
rs2962976	0.85[EUR][1000 genomes]
rs34065204	0.87[EUR][1000 genomes]
rs34809636	0.90[EUR][1000 genomes]
rs34849712	0.91[EUR][1000 genomes]
rs34913883	0.92[EUR][1000 genomes]
rs34932216	0.92[EUR][1000 genomes]
rs34952372	0.92[EUR][1000 genomes]
rs35123365	0.90[EUR][1000 genomes]
rs35265720	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35314830	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35396745	0.91[EUR][1000 genomes]
rs36145010	0.92[EUR][1000 genomes]
rs3857299	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41506252	0.82[JPT][hapmap]
rs4260627	0.89[EUR][1000 genomes]
rs4513649	0.90[TSI][hapmap]
rs4577666	0.85[TSI][hapmap]
rs4700347	0.93[CEU][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs61260776	0.90[EUR][1000 genomes]
rs6874331	0.81[EUR][1000 genomes]
rs6889641	0.89[TSI][hapmap]
rs6896912	0.93[CEU][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.89[EUR][1000 genomes]
rs71627985	0.92[EUR][1000 genomes]
rs71627988	0.90[EUR][1000 genomes]
rs7717864	0.83[GIH][hapmap]
rs977416	1.00[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv1027171	chr5:59267959-59340525	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv881709	chr5:59307813-59437874	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv881710	chr5:59311463-59437874	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16890459	NDUFAF2	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59333200-59337800	Weak transcription	Stomach Mucosa	stomach
2	chr5:59333800-59336200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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