Variant report

Variant	rs28538451
Chromosome Location	chr15:41455769-41455770
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10851403	0.96[EUR][1000 genomes]
rs11852419	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855854	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329235	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13329579	0.95[EUR][1000 genomes]
rs16971454	1.00[ASN][1000 genomes]
rs2448402	0.92[EUR][1000 genomes]
rs28382348	0.95[EUR][1000 genomes]
rs28493087	0.95[EUR][1000 genomes]
rs28516832	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28524914	0.90[EUR][1000 genomes]
rs28551767	1.00[ASN][1000 genomes]
rs28554139	0.89[EUR][1000 genomes]
rs28827035	0.94[EUR][1000 genomes]
rs513280	0.92[EUR][1000 genomes]
rs521890	0.93[EUR][1000 genomes]
rs522063	0.93[EUR][1000 genomes]
rs533210	0.90[EUR][1000 genomes]
rs691011	0.93[EUR][1000 genomes]
rs691629	0.93[EUR][1000 genomes]
rs691906	0.93[EUR][1000 genomes]
rs691907	0.93[EUR][1000 genomes]
rs72737786	0.91[EUR][1000 genomes]
rs72737792	0.91[EUR][1000 genomes]
rs72737793	0.91[EUR][1000 genomes]
rs8038983	0.96[EUR][1000 genomes]
rs8043237	0.91[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	nsv984056	chr15:41455583-41457693	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs28538451	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs28538451	NDUFAF1	cis	Thyroid	GTEx
rs28538451	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs28538451	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs28538451	OIP5-AS1	cis	Artery Tibial	GTEx
rs28538451	NDUFAF1	cis	Muscle Skeletal	GTEx
rs28538451	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs28538451	NDUFAF1	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41454200-41456200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr15:41454800-41456400	Weak transcription	Primary hematopoietic stem cells	blood

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