Variant report

Variant	rs2916860
Chromosome Location	chr5:59278739-59278740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:59278322..59278840-chr5:127773622..127774137,2	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10037011	0.93[EUR][1000 genomes]
rs10044172	0.83[YRI][hapmap];0.88[AFR][1000 genomes]
rs10044529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs10061543	0.89[EUR][1000 genomes]
rs10471471	0.95[AFR][1000 genomes]
rs10514886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514887	0.88[CEU][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs10514902	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs10755240	0.80[ASN][1000 genomes]
rs10805517	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11743973	0.88[CEU][hapmap]
rs11743977	0.81[EUR][1000 genomes]
rs11744029	0.81[EUR][1000 genomes]
rs11745357	0.88[CEU][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs11747070	0.81[EUR][1000 genomes]
rs11960746	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12153039	0.87[CEU][hapmap]
rs12189373	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs12522367	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs13153508	0.88[CEU][hapmap]
rs13160073	0.81[EUR][1000 genomes]
rs13177765	0.82[CEU][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs13177799	0.88[CEU][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs13179177	0.81[EUR][1000 genomes]
rs13184995	0.88[EUR][1000 genomes]
rs13190681	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1369289	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1396476	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1435070	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1435081	1.00[ASN][1000 genomes]
rs1508861	0.88[EUR][1000 genomes]
rs1508863	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs1529842	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs1541961	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs1541962	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890451	0.91[YRI][hapmap]
rs16890455	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs16890459	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]
rs16890516	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs16890521	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs16890523	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs17376533	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs17376568	0.84[MEX][hapmap]
rs17376761	0.88[CEU][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs17376788	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs17442232	0.88[CEU][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs1836543	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876671	0.94[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1946682	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013733	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2117551	0.88[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662432	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2662436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28388570	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2910839	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2916867	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2961898	0.81[EUR][1000 genomes]
rs2961900	0.88[CEU][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs2963812	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34809636	0.81[EUR][1000 genomes]
rs34849712	0.82[EUR][1000 genomes]
rs34913883	0.83[EUR][1000 genomes]
rs34932216	0.83[EUR][1000 genomes]
rs34952372	0.83[EUR][1000 genomes]
rs35123365	0.81[EUR][1000 genomes]
rs35265720	0.82[EUR][1000 genomes]
rs35314830	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35396745	0.82[EUR][1000 genomes]
rs36145010	0.83[EUR][1000 genomes]
rs3857299	0.88[CEU][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs4700347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61260776	0.81[EUR][1000 genomes]
rs6874331	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs6881702	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6896912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71627985	0.83[EUR][1000 genomes]
rs71627988	0.81[EUR][1000 genomes]
rs7446232	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7719560	1.00[ASN][1000 genomes]
rs9292218	0.83[YRI][hapmap];0.88[AFR][1000 genomes]
rs977416	0.82[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2916860	NDUFAF2	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59206400-59278800	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr5:59268200-59287800	Weak transcription	Aorta	Aorta
3	chr5:59272400-59282400	Weak transcription	Primary B cells from cord blood	blood
4	chr5:59273400-59288600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:59278600-59279200	Strong transcription	Primary monocytes fromperipheralblood	blood

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