Variant report

Variant	rs28448670
Chromosome Location	chr15:41600396-41600397
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41574968..41578367-chr15:41600315..41603711,4	K562	blood:
2	chr15:41579631..41582972-chr15:41599254..41603170,4	K562	blood:
3	chr15:41600052..41601763-chr15:41618801..41620323,2	K562	blood:

Variant related genes	Relation type
ENSG00000247556	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10518717	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11070328	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1132639	0.80[EUR][1000 genomes]
rs11629979	0.87[EUR][1000 genomes]
rs11630656	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11635269	0.95[EUR][1000 genomes]
rs11635565	0.91[EUR][1000 genomes]
rs11854081	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11854820	0.89[AMR][1000 genomes]
rs13313520	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17730589	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17730888	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1866399	0.81[EUR][1000 genomes]
rs2118740	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2730056	1.00[AFR][1000 genomes]
rs28377562	0.92[EUR][1000 genomes]
rs28437576	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28458941	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28459164	1.00[AFR][1000 genomes]
rs28463309	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28477406	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28492932	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28493702	0.94[EUR][1000 genomes]
rs28535540	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28557159	0.81[EUR][1000 genomes]
rs28584379	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs28617619	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28623183	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28661013	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28673484	1.00[AFR][1000 genomes]
rs28687846	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28712264	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28716689	0.90[EUR][1000 genomes]
rs28897479	0.86[AMR][1000 genomes]
rs3204853	0.86[AMR][1000 genomes]
rs55725658	1.00[AFR][1000 genomes]
rs56341337	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56400990	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59000092	0.87[EUR][1000 genomes]
rs6493000	0.92[EUR][1000 genomes]
rs7162231	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7163989	0.88[EUR][1000 genomes]
rs7164684	1.00[AFR][1000 genomes]
rs7165396	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7165914	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7167706	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7168002	0.93[AMR][1000 genomes]
rs7168307	0.91[EUR][1000 genomes]
rs7168431	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7169543	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7181982	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7182324	0.90[EUR][1000 genomes]
rs72739630	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72739644	1.00[AFR][1000 genomes]
rs8023530	0.83[EUR][1000 genomes]
rs8030228	0.88[EUR][1000 genomes]
rs8036026	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8037574	0.88[EUR][1000 genomes]
rs8038132	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9568	0.81[AMR][1000 genomes];0.97[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	nsv1045455	chr15:41536624-41620534	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1044438	chr15:41560160-41745480	Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv1038923	chr15:41585028-41754890	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv1045142	chr15:41585044-41738314	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	esv14767	chr15:41595813-41619355	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs28448670	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs28448670	NDUFAF1	cis	lung	GTEx
rs28448670	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs28448670	OIP5-AS1	cis	Nerve Tibial	GTEx
rs28448670	NDUFAF1	cis	Thyroid	GTEx
rs28448670	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs28448670	OIP5-AS1	cis	Artery Tibial	GTEx
rs28448670	OIP5-AS1	cis	Esophagus Mucosa	GTEx
rs28448670	NDUFAF1	cis	Muscle Skeletal	GTEx
rs28448670	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs28448670	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs28448670	OIP5-AS1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41577400-41610600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:41577600-41606400	Weak transcription	Stomach Mucosa	stomach
3	chr15:41579200-41612400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:41580600-41603200	Weak transcription	Psoas Muscle	Psoas
5	chr15:41581200-41601400	Weak transcription	NHDF-Ad	bronchial
6	chr15:41581200-41602200	Weak transcription	Brain Hippocampus Middle	brain
7	chr15:41581200-41602600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr15:41581200-41604800	Weak transcription	Gastric	stomach
9	chr15:41581200-41605000	Weak transcription	Brain Substantia Nigra	brain
10	chr15:41581200-41607000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr15:41581200-41609600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr15:41581200-41623600	Weak transcription	Fetal Brain Male	brain
13	chr15:41581400-41605000	Weak transcription	HMEC	breast
14	chr15:41581400-41610400	Weak transcription	NHLF	lung
15	chr15:41581600-41601800	Weak transcription	Fetal Lung	lung
16	chr15:41581600-41623600	Weak transcription	Fetal Kidney	kidney
17	chr15:41583200-41623600	Weak transcription	HSMM	muscle
18	chr15:41583800-41613000	Weak transcription	Right Ventricle	heart
19	chr15:41584000-41604800	Weak transcription	Aorta	Aorta
20	chr15:41585000-41602800	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:41585600-41623600	Weak transcription	Primary B cells from cord blood	blood
22	chr15:41587200-41606800	Weak transcription	Fetal Heart	heart
23	chr15:41587600-41623000	Weak transcription	NHEK	skin
24	chr15:41588400-41600600	Weak transcription	Hela-S3	cervix
25	chr15:41589400-41601800	Weak transcription	K562	blood
26	chr15:41589400-41603600	Weak transcription	Spleen	Spleen
27	chr15:41589400-41604800	Weak transcription	Pancreas	Pancrea
28	chr15:41589600-41604800	Weak transcription	Lung	lung
29	chr15:41589600-41624000	Weak transcription	Esophagus	oesophagus
30	chr15:41590200-41601800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr15:41590200-41609200	Weak transcription	Colonic Mucosa	Colon
32	chr15:41590200-41623600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr15:41590600-41601800	Weak transcription	Primary T cells from cord blood	blood
34	chr15:41590600-41602000	Weak transcription	Brain Germinal Matrix	brain
35	chr15:41590600-41603000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr15:41590600-41606800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:41590600-41623000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr15:41590800-41623000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr15:41591000-41606600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:41591200-41605000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr15:41591200-41623800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr15:41591200-41624000	Weak transcription	HSMMtube	muscle
43	chr15:41591600-41600600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr15:41591600-41601000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr15:41591600-41601800	Weak transcription	Left Ventricle	heart
46	chr15:41591600-41602400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:41591600-41606600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr15:41591600-41611400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:41591600-41623200	Weak transcription	HUVEC	blood vessel
50	chr15:41591800-41600600	Weak transcription	Fetal Stomach	stomach

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