Variant report

Variant	rs977416
Chromosome Location	chr5:59232622-59232623
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10037011	0.84[EUR][1000 genomes]
rs10044529	0.84[EUR][1000 genomes]
rs10061543	0.83[EUR][1000 genomes]
rs10069878	1.00[JPT][hapmap]
rs10514886	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10514887	0.84[MEX][hapmap]
rs10514888	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10755240	0.81[EUR][1000 genomes]
rs11745357	0.84[MEX][hapmap]
rs11960746	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13156502	1.00[JPT][hapmap]
rs13177765	1.00[MEX][hapmap];0.80[TSI][hapmap]
rs13177799	1.00[MEX][hapmap];0.80[TSI][hapmap]
rs1369289	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1529842	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541961	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541962	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1546364	1.00[JPT][hapmap]
rs16890369	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16890455	0.82[EUR][1000 genomes]
rs16890459	1.00[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs17376568	0.84[MEX][hapmap]
rs17376761	0.84[MEX][hapmap]
rs17442232	1.00[MEX][hapmap];0.80[TSI][hapmap]
rs1836543	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1876671	1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs1946682	0.90[EUR][1000 genomes]
rs2117551	1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2662436	0.90[EUR][1000 genomes]
rs28388570	0.83[EUR][1000 genomes]
rs2916860	0.82[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs34918713	0.85[ASN][1000 genomes]
rs35314830	0.85[EUR][1000 genomes]
rs3857299	1.00[MEX][hapmap];0.80[TSI][hapmap]
rs4700347	0.82[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61576239	0.84[ASN][1000 genomes]
rs6450536	1.00[JPT][hapmap]
rs6874331	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6879288	0.85[ASN][1000 genomes]
rs6896912	0.82[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7710463	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1018431	chr5:59191099-59265363	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1034311	chr5:59193517-59257171	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1016184	chr5:59199687-59251169	Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv537768	chr5:59199687-59251169	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs977416	NDUFAF2	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59206400-59278800	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr5:59232200-59232800	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr5:59232600-59232800	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr5:59232600-59233400	Enhancers	HUES48 Cell Line	embryonic stem cell

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