Variant report

Variant	rs28828670
Chromosome Location	chr15:41434041-41434042
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11853192	0.86[EUR][1000 genomes]
rs11855797	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11858678	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12101934	0.82[EUR][1000 genomes]
rs12324159	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1659227	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1678750	0.81[ASN][1000 genomes]
rs1717198	0.81[EUR][1000 genomes]
rs1983400	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2176998	0.85[ASN][1000 genomes]
rs2412601	0.82[ASN][1000 genomes]
rs2578655	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28409432	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28455998	0.89[ASN][1000 genomes]
rs28510775	0.85[EUR][1000 genomes]
rs28516683	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28613002	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28688742	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28729675	0.89[ASN][1000 genomes]
rs28866311	0.89[ASN][1000 genomes]
rs2899013	0.83[EUR][1000 genomes]
rs2928148	0.81[ASN][1000 genomes]
rs2928156	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2947493	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2947494	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36046988	0.83[EUR][1000 genomes]
rs4592624	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs476633	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs537244	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs551482	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs561301	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57393155	0.89[ASN][1000 genomes]
rs61203391	0.82[EUR][1000 genomes]
rs6492983	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6492991	0.80[EUR][1000 genomes]
rs66818965	0.81[ASN][1000 genomes]
rs690733	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs691672	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs691702	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs692153	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs692195	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7170049	0.83[EUR][1000 genomes]
rs7173841	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7180853	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8027932	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8033435	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9888710	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9888718	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9972349	0.83[EUR][1000 genomes]
rs9972622	0.83[EUR][1000 genomes]

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	nsv569229	chr15:41361138-41483682	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv904107	chr15:41361138-41493013	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers 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	38 gene(s)	inside rSNPs	diseases
3	nsv569230	chr15:41384649-41483682	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv904108	chr15:41384649-41486990	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv904109	chr15:41410705-41481254	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv457120	chr15:41410705-41546631	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv569231	chr15:41410705-41546631	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv10980	chr15:41423683-41445889	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28828670	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41431800-41434400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:41434000-41434400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr15:41434000-41434600	Enhancers	Hela-S3	cervix

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