Variant report

Variant	rs3857299
Chromosome Location	chr5:59355381-59355382
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10037011	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10044529	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10061543	0.92[EUR][1000 genomes]
rs10514886	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs10514887	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs10514902	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs11742066	0.87[EUR][1000 genomes]
rs11743973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs11743977	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11744029	0.93[EUR][1000 genomes]
rs11745357	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs11747070	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11960746	0.86[EUR][1000 genomes]
rs12153039	1.00[CEU][hapmap]
rs12188020	0.85[TSI][hapmap]
rs12189373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12522367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13153508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13157125	0.90[TSI][hapmap]
rs13160073	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13175365	0.90[EUR][1000 genomes]
rs13177765	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13177799	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs13179177	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13184995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13190681	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1369289	0.86[EUR][1000 genomes]
rs1396476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1508861	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1508863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1541962	0.82[EUR][1000 genomes]
rs16890455	0.94[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs16890459	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]
rs16890516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs16890521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16890523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs17376533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs17376568	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs17376761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs17376788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs17442232	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[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	0.86[EUR][1000 genomes]
rs1876671	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1946682	1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2013733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2117551	1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2662436	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs28388570	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2910835	0.88[EUR][1000 genomes]
rs2910836	0.88[EUR][1000 genomes]
rs2910837	0.88[EUR][1000 genomes]
rs2910839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs2916860	0.88[CEU][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs2961898	0.92[EUR][1000 genomes]
rs2961899	0.91[EUR][1000 genomes]
rs2961900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs2962963	0.91[EUR][1000 genomes]
rs2962976	0.88[EUR][1000 genomes]
rs34065204	0.89[EUR][1000 genomes]
rs34809636	0.93[EUR][1000 genomes]
rs34849712	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs34913883	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs34932216	0.95[EUR][1000 genomes]
rs34952372	0.95[EUR][1000 genomes]
rs35123365	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs35265720	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35314830	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35396745	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs36145010	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs41506252	0.82[JPT][hapmap]
rs4260627	0.91[EUR][1000 genomes]
rs4513649	0.90[TSI][hapmap]
rs4577666	0.85[TSI][hapmap]
rs4700347	0.88[CEU][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs61260776	0.93[EUR][1000 genomes]
rs6889641	0.89[TSI][hapmap]
rs6896912	0.88[CEU][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs71627985	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs71627988	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7717864	0.83[GIH][hapmap]
rs977416	1.00[MEX][hapmap];0.80[TSI][hapmap]

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	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
6	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
7	nsv508361	chr5:59336428-59365985	Enhancers Weak transcription Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3857299	NDUFAF2	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59355000-59355600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr5:59355200-59355800	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr5:59355200-59359400	Weak transcription	Fetal Brain Male	brain

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