Variant report

Variant	rs1132639
Chromosome Location	chr15:41597437-41597438
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41593303..41595155-chr15:41597240..41599899,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC012652.1.1-1	chr15:41590239-41598727	XLOC_011226
2	lnc-AC012652.1.1-1	chr15:41590239-41598727	XLOC_011226
3	lnc-AC012652.1.1-1	chr15:41594573-41598729	NONHSAT041936
4	lnc-OIP5-1	chr15:41588773-41598741	XLOC_011448

Extended variants
information (count: 20 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11629979	0.83[EUR][1000 genomes]
rs17730589	0.80[EUR][1000 genomes]
rs28377562	0.86[EUR][1000 genomes]
rs28437576	0.80[EUR][1000 genomes]
rs28448670	0.80[EUR][1000 genomes]
rs28687846	0.80[EUR][1000 genomes]
rs28712264	0.81[EUR][1000 genomes]
rs59000092	0.83[EUR][1000 genomes]
rs6493000	0.86[EUR][1000 genomes]
rs7162231	0.81[EUR][1000 genomes]
rs7163989	0.83[EUR][1000 genomes]
rs7168307	0.85[EUR][1000 genomes]
rs7182324	0.84[EUR][1000 genomes]
rs8030228	0.83[EUR][1000 genomes]
rs8037574	0.82[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
rs1132639	NDUFAF1	cis	multi-tissue	Pritchard
rs1132639	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs1132639	OIP5-AS1	cis	Esophagus Mucosa	GTEx
rs1132639	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs1132639	NDUFAF1	cis	Muscle Skeletal	GTEx
rs1132639	OIP5-AS1	cis	Esophagus Muscularis	GTEx
rs1132639	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs1132639	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs1132639	NDUFAF1	cis	Thyroid	GTEx
rs1132639	OIP5-AS1	cis	Nerve Tibial	GTEx
rs1132639	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs1132639	LOC729082	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 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	chr15:41581200-41598400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr15:41581200-41601400	Weak transcription	NHDF-Ad	bronchial
7	chr15:41581200-41602200	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:41581200-41602600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr15:41581200-41604800	Weak transcription	Gastric	stomach
10	chr15:41581200-41605000	Weak transcription	Brain Substantia Nigra	brain
11	chr15:41581200-41607000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:41581200-41609600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr15:41581200-41623600	Weak transcription	Fetal Brain Male	brain
14	chr15:41581400-41605000	Weak transcription	HMEC	breast
15	chr15:41581400-41610400	Weak transcription	NHLF	lung
16	chr15:41581600-41601800	Weak transcription	Fetal Lung	lung
17	chr15:41581600-41623600	Weak transcription	Fetal Kidney	kidney
18	chr15:41583200-41623600	Weak transcription	HSMM	muscle
19	chr15:41583800-41613000	Weak transcription	Right Ventricle	heart
20	chr15:41584000-41604800	Weak transcription	Aorta	Aorta
21	chr15:41585000-41602800	Weak transcription	Colon Smooth Muscle	Colon
22	chr15:41585600-41623600	Weak transcription	Primary B cells from cord blood	blood
23	chr15:41587200-41606800	Weak transcription	Fetal Heart	heart
24	chr15:41587600-41623000	Weak transcription	NHEK	skin
25	chr15:41588400-41600600	Weak transcription	Hela-S3	cervix
26	chr15:41589400-41601800	Weak transcription	K562	blood
27	chr15:41589400-41603600	Weak transcription	Spleen	Spleen
28	chr15:41589400-41604800	Weak transcription	Pancreas	Pancrea
29	chr15:41589600-41604800	Weak transcription	Lung	lung
30	chr15:41589600-41624000	Weak transcription	Esophagus	oesophagus
31	chr15:41590200-41601800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:41590200-41609200	Weak transcription	Colonic Mucosa	Colon
33	chr15:41590200-41623600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr15:41590400-41600000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:41590600-41601800	Weak transcription	Primary T cells from cord blood	blood
36	chr15:41590600-41602000	Weak transcription	Brain Germinal Matrix	brain
37	chr15:41590600-41603000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr15:41590600-41606800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr15:41590600-41623000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr15:41590800-41623000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr15:41591000-41606600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr15:41591200-41605000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr15:41591200-41623800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:41591200-41624000	Weak transcription	HSMMtube	muscle
45	chr15:41591600-41599800	Weak transcription	Fetal Intestine Small	intestine
46	chr15:41591600-41600600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr15:41591600-41601000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr15:41591600-41601800	Weak transcription	Left Ventricle	heart
49	chr15:41591600-41602400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:41591600-41606600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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