Variant report

Variant	rs28459164
Chromosome Location	chr15:41717313-41717314
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11070328	0.83[EUR][1000 genomes]
rs11630656	1.00[AFR][1000 genomes]
rs11630799	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11635906	0.86[EUR][1000 genomes]
rs11854081	0.83[EUR][1000 genomes]
rs11854632	0.93[EUR][1000 genomes]
rs11854820	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11858068	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11858812	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1757468	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17730888	0.80[EUR][1000 genomes]
rs1899	0.95[EUR][1000 genomes]
rs2118740	0.83[AFR][1000 genomes]
rs2730056	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2730058	0.93[EUR][1000 genomes]
rs28416360	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28421136	0.95[EUR][1000 genomes]
rs28448670	1.00[AFR][1000 genomes]
rs28456082	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28458941	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28463309	0.84[EUR][1000 genomes]
rs28477406	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs28535540	0.86[EUR][1000 genomes]
rs28555198	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28576457	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28584379	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28623183	0.80[EUR][1000 genomes]
rs28661013	0.86[EUR][1000 genomes]
rs28663426	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28673484	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28700583	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28703570	0.95[EUR][1000 genomes]
rs28897479	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs316604	0.84[EUR][1000 genomes]
rs316606	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs316607	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs316611	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs316616	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3204853	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34040639	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34285452	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34665396	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55725658	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56400990	0.84[EUR][1000 genomes]
rs6493003	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7164211	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7164684	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7168002	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7168431	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72739630	1.00[AFR][1000 genomes]
rs72739644	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8034840	0.94[EUR][1000 genomes]
rs8036734	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8041809	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1039283	chr15:41620499-41745480	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
5	nsv933757	chr15:41641236-41773058	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
6	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv569232	chr15:41694377-41730246	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs28459164	NDUFAF1	cis	Thyroid	GTEx
rs28459164	OIP5-AS1	cis	Nerve Tibial	GTEx
rs28459164	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs28459164	OIP5-AS1	cis	Artery Tibial	GTEx
rs28459164	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs28459164	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs28459164	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs28459164	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs28459164	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs28459164	NDUFAF1	cis	Muscle Skeletal	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41710400-41724600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:41710400-41745200	Weak transcription	Esophagus	oesophagus
3	chr15:41710400-41750000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:41710600-41721200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:41710600-41721200	Weak transcription	Right Atrium	heart
6	chr15:41710600-41723800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:41710600-41723800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:41710600-41729800	Weak transcription	Brain Substantia Nigra	brain
9	chr15:41710600-41731600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr15:41710600-41731600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:41710600-41731800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr15:41710600-41733600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr15:41710600-41745200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:41710800-41718800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr15:41710800-41718800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr15:41710800-41718800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr15:41710800-41718800	Weak transcription	HMEC	breast
18	chr15:41710800-41718800	Weak transcription	NH-A	brain
19	chr15:41710800-41718800	Weak transcription	NHLF	lung
20	chr15:41710800-41720800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:41710800-41720800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr15:41710800-41721200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:41710800-41724200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:41710800-41724800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:41710800-41724800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr15:41710800-41726600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr15:41710800-41727800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr15:41710800-41729800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr15:41710800-41729800	Weak transcription	Psoas Muscle	Psoas
30	chr15:41710800-41730200	Weak transcription	Fetal Intestine Large	intestine
31	chr15:41710800-41730600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr15:41710800-41731600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:41710800-41731800	Weak transcription	Left Ventricle	heart
34	chr15:41710800-41733400	Weak transcription	Brain Hippocampus Middle	brain
35	chr15:41710800-41733400	Weak transcription	HSMMtube	muscle
36	chr15:41711000-41718800	Weak transcription	HSMM	muscle
37	chr15:41711000-41729800	Weak transcription	Placenta	Placenta
38	chr15:41711000-41730200	Weak transcription	Adipose Nuclei	Adipose
39	chr15:41711000-41730600	Weak transcription	Osteobl	bone
40	chr15:41711200-41718800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr15:41711200-41721200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr15:41711200-41722600	Weak transcription	Fetal Muscle Leg	muscle
43	chr15:41711200-41723800	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr15:41711200-41724000	Weak transcription	Thymus	Thymus
45	chr15:41711200-41724400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:41711200-41727800	Weak transcription	Fetal Thymus	thymus
47	chr15:41711400-41718800	Weak transcription	Primary T cells from cord blood	blood
48	chr15:41711400-41723600	Weak transcription	Fetal Intestine Small	intestine
49	chr15:41711400-41730600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr15:41711400-41733400	Weak transcription	Brain Angular Gyrus	brain

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