Variant report

Variant	rs7167729
Chromosome Location	chr15:41721042-41721043
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10152497	0.91[ASN][1000 genomes]
rs10153010	0.91[ASN][1000 genomes]
rs10467974	0.82[ASN][1000 genomes]
rs10518718	0.86[ASN][1000 genomes]
rs11630191	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11631770	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11633799	0.83[ASN][1000 genomes]
rs12324291	0.88[ASN][1000 genomes]
rs1655556	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1655557	0.82[EUR][1000 genomes]
rs16971767	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16971798	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16971806	0.96[ASN][1000 genomes]
rs16971832	0.84[ASN][1000 genomes]
rs16971834	0.83[ASN][1000 genomes]
rs1757455	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2015781	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2777491	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28393472	0.91[ASN][1000 genomes]
rs28526381	0.88[ASN][1000 genomes]
rs28578057	0.88[ASN][1000 genomes]
rs28583065	0.88[ASN][1000 genomes]
rs28600680	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28643296	0.84[ASN][1000 genomes]
rs28655070	0.93[ASN][1000 genomes]
rs28716108	0.91[ASN][1000 genomes]
rs28792672	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28847691	0.91[ASN][1000 genomes]
rs316605	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs316609	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs316610	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs316613	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs316614	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs316615	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316617	0.81[EUR][1000 genomes]
rs35826725	0.95[ASN][1000 genomes]
rs3743038	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55782852	0.88[ASN][1000 genomes]
rs58335029	0.80[ASN][1000 genomes]
rs58910172	0.84[ASN][1000 genomes]
rs59590312	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61037359	0.87[ASN][1000 genomes]
rs61127691	0.84[ASN][1000 genomes]
rs6650519	0.86[ASN][1000 genomes]
rs66538814	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66591771	0.85[EUR][1000 genomes]
rs7161772	0.88[ASN][1000 genomes]
rs7163649	0.87[ASN][1000 genomes]
rs7163788	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165675	0.88[ASN][1000 genomes]
rs7167498	0.83[ASN][1000 genomes]
rs7168177	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7172148	0.95[ASN][1000 genomes]
rs7175690	0.84[ASN][1000 genomes]
rs7175800	0.84[ASN][1000 genomes]
rs7176314	0.84[ASN][1000 genomes]
rs7176505	0.81[ASN][1000 genomes]
rs7176588	0.87[ASN][1000 genomes]
rs7177641	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7180492	0.86[ASN][1000 genomes]
rs7181560	0.83[ASN][1000 genomes]
rs7181911	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7182667	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7182700	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7183337	0.80[ASN][1000 genomes]
rs73404980	0.80[ASN][1000 genomes]
rs73404987	0.86[ASN][1000 genomes]
rs73404994	0.91[ASN][1000 genomes]
rs73404995	0.91[ASN][1000 genomes]
rs73404996	0.91[ASN][1000 genomes]
rs73405000	0.88[ASN][1000 genomes]
rs73405001	0.88[ASN][1000 genomes]
rs73407109	0.91[ASN][1000 genomes]
rs8023619	0.81[ASN][1000 genomes]
rs8026197	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027626	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8032838	0.88[ASN][1000 genomes]
rs8034626	0.86[ASN][1000 genomes]
rs8034819	0.95[ASN][1000 genomes]
rs8036498	0.88[ASN][1000 genomes]
rs8036527	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8037824	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs823716	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs919961	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9302109	0.88[ASN][1000 genomes]
rs9672866	0.87[ASN][1000 genomes]
rs9972288	0.90[EUR][1000 genomes];0.92[ASN][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7167729	OIP5-AS1	cis	Artery Tibial	GTEx
rs7167729	NDUFAF1	cis	Muscle Skeletal	GTEx
rs7167729	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs7167729	OIP5-AS1	cis	Nerve Tibial	GTEx
rs7167729	NDUFAF1	cis	Thyroid	GTEx
rs7167729	NDUFAF1	cis	multi-tissue	Pritchard
rs7167729	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs7167729	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs7167729	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs7167729	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs7167729	NDUFAF1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:113 , 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	chr15:41710800-41721200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr15:41710800-41724200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:41710800-41724800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:41710800-41724800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr15:41710800-41726600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr15:41710800-41727800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:41710800-41729800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr15:41710800-41729800	Weak transcription	Psoas Muscle	Psoas
22	chr15:41710800-41730200	Weak transcription	Fetal Intestine Large	intestine
23	chr15:41710800-41730600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr15:41710800-41731600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:41710800-41731800	Weak transcription	Left Ventricle	heart
26	chr15:41710800-41733400	Weak transcription	Brain Hippocampus Middle	brain
27	chr15:41710800-41733400	Weak transcription	HSMMtube	muscle
28	chr15:41711000-41729800	Weak transcription	Placenta	Placenta
29	chr15:41711000-41730200	Weak transcription	Adipose Nuclei	Adipose
30	chr15:41711000-41730600	Weak transcription	Osteobl	bone
31	chr15:41711200-41721200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:41711200-41722600	Weak transcription	Fetal Muscle Leg	muscle
33	chr15:41711200-41723800	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr15:41711200-41724000	Weak transcription	Thymus	Thymus
35	chr15:41711200-41724400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:41711200-41727800	Weak transcription	Fetal Thymus	thymus
37	chr15:41711400-41723600	Weak transcription	Fetal Intestine Small	intestine
38	chr15:41711400-41730600	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:41711400-41733400	Weak transcription	Brain Angular Gyrus	brain
40	chr15:41711400-41733400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr15:41711600-41725000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:41711600-41731000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:41711600-41746800	Weak transcription	A549	lung
44	chr15:41711600-41759000	Weak transcription	Fetal Heart	heart
45	chr15:41711800-41735400	Weak transcription	Fetal Kidney	kidney
46	chr15:41712800-41733600	Weak transcription	Fetal Lung	lung
47	chr15:41713200-41723800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr15:41713200-41724600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:41713200-41730400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:41713200-41745200	Weak transcription	Spleen	Spleen

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