Variant report

Variant	rs28382348
Chromosome Location	chr15:41487934-41487935
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr15:41487844-41488322	HepG2	liver:	n/a	chr15:41487987-41488002
2	MAFK	chr15:41487895-41488291	HepG2	liver:	n/a	chr15:41487987-41488002
3	MAFF	chr15:41487854-41488215	HepG2	liver:	n/a	chr15:41487986-41488004
4	MAFK	chr15:41487913-41488345	IMR90	lung:	n/a	chr15:41487987-41488002

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC012652.1.1-4	chr15:41487791-41489261	predAs_engstrom06_AA009975_1

Variant related genes	Relation type
RN7SL497P	TF binding region

Extended variants
information (count: 94 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10518717	1.00[ASN][1000 genomes]
rs10851403	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070328	1.00[ASN][1000 genomes]
rs11629979	1.00[ASN][1000 genomes]
rs11630656	1.00[ASN][1000 genomes]
rs11635269	1.00[ASN][1000 genomes]
rs11635565	1.00[ASN][1000 genomes]
rs11852419	0.95[EUR][1000 genomes]
rs11854081	1.00[ASN][1000 genomes]
rs11854632	1.00[ASN][1000 genomes]
rs11854820	1.00[ASN][1000 genomes]
rs11855854	0.91[EUR][1000 genomes]
rs11855906	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11856169	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13313520	1.00[ASN][1000 genomes]
rs13329235	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329579	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730589	1.00[ASN][1000 genomes]
rs17730888	1.00[ASN][1000 genomes]
rs1866399	1.00[ASN][1000 genomes]
rs1899	1.00[ASN][1000 genomes]
rs2118740	1.00[ASN][1000 genomes]
rs2448402	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28374715	0.81[EUR][1000 genomes]
rs28377562	1.00[ASN][1000 genomes]
rs28421136	1.00[ASN][1000 genomes]
rs28437576	1.00[ASN][1000 genomes]
rs28458941	1.00[ASN][1000 genomes]
rs28463309	1.00[ASN][1000 genomes]
rs28477406	1.00[ASN][1000 genomes]
rs28492932	1.00[ASN][1000 genomes]
rs28493087	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493702	1.00[ASN][1000 genomes]
rs28516832	0.81[EUR][1000 genomes]
rs28524914	0.95[EUR][1000 genomes]
rs28535540	1.00[ASN][1000 genomes]
rs28538451	0.95[EUR][1000 genomes]
rs28554139	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28555198	1.00[ASN][1000 genomes]
rs28557159	1.00[ASN][1000 genomes]
rs28584379	1.00[ASN][1000 genomes]
rs28617619	1.00[ASN][1000 genomes]
rs28623183	1.00[ASN][1000 genomes]
rs28661013	1.00[ASN][1000 genomes]
rs28671712	0.81[EUR][1000 genomes]
rs28687846	1.00[ASN][1000 genomes]
rs28703570	1.00[ASN][1000 genomes]
rs28712264	1.00[ASN][1000 genomes]
rs28716689	1.00[ASN][1000 genomes]
rs28827035	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28897479	1.00[ASN][1000 genomes]
rs3204853	1.00[ASN][1000 genomes]
rs513280	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521890	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs522063	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533210	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56400990	1.00[ASN][1000 genomes]
rs59000092	1.00[ASN][1000 genomes]
rs6493000	1.00[ASN][1000 genomes]
rs691011	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs691629	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs691906	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs691907	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162231	1.00[ASN][1000 genomes]
rs7163989	1.00[ASN][1000 genomes]
rs7164211	1.00[ASN][1000 genomes]
rs7164684	1.00[ASN][1000 genomes]
rs7165396	1.00[ASN][1000 genomes]
rs7165914	1.00[ASN][1000 genomes]
rs7167706	1.00[ASN][1000 genomes]
rs7168002	1.00[ASN][1000 genomes]
rs7168307	1.00[ASN][1000 genomes]
rs7168431	1.00[ASN][1000 genomes]
rs7169543	1.00[ASN][1000 genomes]
rs7181982	1.00[ASN][1000 genomes]
rs7182324	1.00[ASN][1000 genomes]
rs72737786	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737792	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737793	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72739630	1.00[ASN][1000 genomes]
rs8023530	1.00[ASN][1000 genomes]
rs8034840	1.00[ASN][1000 genomes]
rs8036026	1.00[ASN][1000 genomes]
rs8036734	1.00[ASN][1000 genomes]
rs8037574	1.00[ASN][1000 genomes]
rs8038132	1.00[ASN][1000 genomes]
rs8038983	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041809	1.00[ASN][1000 genomes]
rs8043237	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1039906	chr15:41476209-41518976	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs28382348	NDUFAF1	cis	Thyroid	GTEx
rs28382348	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs28382348	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs28382348	NDUFAF1	cis	multi-tissue	Pritchard
rs28382348	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs28382348	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs28382348	NDUFAF1	cis	Muscle Skeletal	GTEx
rs28382348	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs28382348	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41484400-41494400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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