Variant report

Variant	rs7165396
Chromosome Location	chr15:41586947-41586948
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10518717	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851403	1.00[ASN][1000 genomes]
rs11070328	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629979	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630656	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630799	1.00[ASN][1000 genomes]
rs11635269	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635565	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635906	1.00[ASN][1000 genomes]
rs11854081	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854632	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11854820	1.00[ASN][1000 genomes]
rs11858068	1.00[ASN][1000 genomes]
rs11858812	1.00[ASN][1000 genomes]
rs13313520	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329235	1.00[ASN][1000 genomes]
rs13329579	1.00[ASN][1000 genomes]
rs1757468	1.00[ASN][1000 genomes]
rs17730589	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730888	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866399	1.00[ASN][1000 genomes]
rs1899	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2118740	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448402	1.00[ASN][1000 genomes]
rs2730056	1.00[ASN][1000 genomes]
rs2730058	1.00[ASN][1000 genomes]
rs28377562	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382348	1.00[ASN][1000 genomes]
rs28416360	1.00[ASN][1000 genomes]
rs28421136	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28437576	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28448670	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28456082	1.00[ASN][1000 genomes]
rs28458941	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28463309	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477406	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492932	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493087	1.00[ASN][1000 genomes]
rs28493702	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535540	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28555198	1.00[ASN][1000 genomes]
rs28557159	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28576457	1.00[ASN][1000 genomes]
rs28584379	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28617619	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28623183	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661013	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663426	1.00[ASN][1000 genomes]
rs28673484	1.00[ASN][1000 genomes]
rs28687846	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28700583	1.00[ASN][1000 genomes]
rs28703570	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28712264	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716689	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28827035	1.00[ASN][1000 genomes]
rs28897479	1.00[ASN][1000 genomes]
rs316604	1.00[ASN][1000 genomes]
rs316606	1.00[ASN][1000 genomes]
rs316607	1.00[ASN][1000 genomes]
rs316611	1.00[ASN][1000 genomes]
rs316616	1.00[ASN][1000 genomes]
rs3204853	1.00[ASN][1000 genomes]
rs34665396	1.00[ASN][1000 genomes]
rs513280	1.00[ASN][1000 genomes]
rs521890	1.00[ASN][1000 genomes]
rs522063	1.00[ASN][1000 genomes]
rs55725658	1.00[ASN][1000 genomes]
rs56341337	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56400990	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59000092	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493000	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493003	1.00[ASN][1000 genomes]
rs691011	1.00[ASN][1000 genomes]
rs691906	1.00[ASN][1000 genomes]
rs691907	1.00[ASN][1000 genomes]
rs7162231	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163989	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164211	1.00[ASN][1000 genomes]
rs7164684	1.00[ASN][1000 genomes]
rs7165914	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167706	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168002	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7168307	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168431	1.00[ASN][1000 genomes]
rs7169543	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181982	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182324	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737786	1.00[ASN][1000 genomes]
rs72737792	1.00[ASN][1000 genomes]
rs72737793	1.00[ASN][1000 genomes]
rs72739630	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72739644	1.00[ASN][1000 genomes]
rs8023530	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030228	0.86[EUR][1000 genomes]
rs8034840	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8036026	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036734	1.00[ASN][1000 genomes]
rs8037574	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038132	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038983	1.00[ASN][1000 genomes]
rs8041809	1.00[ASN][1000 genomes]
rs8043237	1.00[ASN][1000 genomes]
rs9568	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][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	esv3424205	chr15:41586900-41587742	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7165396	OIP5-AS1	cis	Esophagus Mucosa	GTEx
rs7165396	OIP5-AS1	cis	Artery Tibial	GTEx
rs7165396	OIP5-AS1	cis	Nerve Tibial	GTEx
rs7165396	NDUFAF1	cis	Thyroid	GTEx
rs7165396	NDUFAF1	cis	lung	GTEx
rs7165396	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs7165396	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs7165396	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs7165396	NDUFAF1	cis	multi-tissue	Pritchard
rs7165396	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs7165396	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs7165396	NDUFAF1	cis	Muscle Skeletal	GTEx
rs7165396	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 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	chr15:41577800-41589000	Weak transcription	Esophagus	oesophagus
4	chr15:41577800-41591600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:41578000-41588400	Weak transcription	Right Atrium	heart
6	chr15:41578000-41591600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:41578200-41591800	Strong transcription	Fetal Stomach	stomach
8	chr15:41578200-41592600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr15:41578400-41592600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr15:41578800-41587800	Strong transcription	Fetal Muscle Leg	muscle
11	chr15:41578800-41591800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:41579200-41593200	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr15:41579200-41612400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:41580000-41592600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:41580600-41603200	Weak transcription	Psoas Muscle	Psoas
16	chr15:41581000-41588400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:41581000-41590000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:41581000-41593200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr15:41581200-41587000	Weak transcription	Brain Germinal Matrix	brain
20	chr15:41581200-41587600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:41581200-41588200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr15:41581200-41589000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr15:41581200-41589000	Weak transcription	Ovary	ovary
24	chr15:41581200-41589000	Weak transcription	Spleen	Spleen
25	chr15:41581200-41589000	Weak transcription	HSMMtube	muscle
26	chr15:41581200-41589200	Weak transcription	Colonic Mucosa	Colon
27	chr15:41581200-41589200	Weak transcription	Pancreas	Pancrea
28	chr15:41581200-41592200	Weak transcription	Brain Angular Gyrus	brain
29	chr15:41581200-41592200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr15:41581200-41592400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr15:41581200-41593000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr15:41581200-41595200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr15:41581200-41596000	Weak transcription	Small Intestine	intestine
34	chr15:41581200-41598400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr15:41581200-41601400	Weak transcription	NHDF-Ad	bronchial
36	chr15:41581200-41602200	Weak transcription	Brain Hippocampus Middle	brain
37	chr15:41581200-41602600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr15:41581200-41604800	Weak transcription	Gastric	stomach
39	chr15:41581200-41605000	Weak transcription	Brain Substantia Nigra	brain
40	chr15:41581200-41607000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr15:41581200-41609600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr15:41581200-41623600	Weak transcription	Fetal Brain Male	brain
43	chr15:41581400-41589200	Weak transcription	HUVEC	blood vessel
44	chr15:41581400-41605000	Weak transcription	HMEC	breast
45	chr15:41581400-41610400	Weak transcription	NHLF	lung
46	chr15:41581600-41588400	Strong transcription	Dnd41	blood
47	chr15:41581600-41589000	Weak transcription	Brain Anterior Caudate	brain
48	chr15:41581600-41589200	Weak transcription	Placenta	Placenta
49	chr15:41581600-41589400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:41581600-41589800	Weak transcription	Muscle Satellite Cultured Cells	--

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