Variant report

Variant	rs55817686
Chromosome Location	chr5:41734112-41734113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10941559	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11738517	0.92[EUR][1000 genomes]
rs11739106	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11739257	0.97[EUR][1000 genomes]
rs11740524	0.95[EUR][1000 genomes]
rs11740946	0.99[EUR][1000 genomes]
rs11742249	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11744279	0.99[EUR][1000 genomes]
rs11744516	0.99[EUR][1000 genomes]
rs11744623	0.96[EUR][1000 genomes]
rs11746511	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11747881	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11747921	0.99[EUR][1000 genomes]
rs11749008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11750607	0.88[EUR][1000 genomes]
rs11750760	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11750790	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13153468	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13153837	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13155013	0.85[EUR][1000 genomes]
rs13155338	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13156367	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13162040	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13163137	0.99[EUR][1000 genomes]
rs13164201	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13165731	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13167578	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13168035	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13169285	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13169977	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13170096	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13176368	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13177937	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13179852	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13180405	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13180475	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13182336	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13185973	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13186086	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13189403	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1345781	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1389756	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1508815	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1508818	0.88[EUR][1000 genomes]
rs16871955	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16871972	0.97[EUR][1000 genomes]
rs16900142	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1876653	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1876654	0.94[EUR][1000 genomes]
rs2081102	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs33967331	0.99[EUR][1000 genomes]
rs34048302	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34071445	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34193394	0.87[EUR][1000 genomes]
rs34329864	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34339137	0.99[EUR][1000 genomes]
rs34369972	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34412181	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34500930	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34569700	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34625465	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34663371	0.99[EUR][1000 genomes]
rs34841703	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34873414	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34898214	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35077044	0.99[EUR][1000 genomes]
rs35244816	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35252930	0.99[EUR][1000 genomes]
rs35343042	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35613904	0.96[EUR][1000 genomes]
rs35691805	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35748945	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35764180	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35861205	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs36005620	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs36009913	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36113900	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3926618	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4957430	0.97[EUR][1000 genomes]
rs56017638	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60209308	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62360521	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62360542	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs66820325	0.97[EUR][1000 genomes]
rs67114999	0.99[EUR][1000 genomes]
rs67206815	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67715253	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67869805	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6866549	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6879341	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6881206	0.83[EUR][1000 genomes]
rs6881873	0.97[EUR][1000 genomes]
rs6883144	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6888816	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6889217	0.99[EUR][1000 genomes]
rs72746918	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72746919	1.00[EUR][1000 genomes]
rs72746957	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7709500	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7712911	0.93[EUR][1000 genomes]
rs7724934	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7725264	0.86[EUR][1000 genomes]
rs951883	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs964267	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9687619	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9763018	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3404444	chr5:41701527-41744979	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
2	esv3326078	chr5:41710992-41743453	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv830271	chr5:41716527-41895710	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55817686	OXCT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41722000-41736800	Weak transcription	HSMMtube	muscle
2	chr5:41723000-41735800	Weak transcription	GM12878-XiMat	blood
3	chr5:41723000-41739200	Weak transcription	Aorta	Aorta
4	chr5:41725400-41739200	Weak transcription	Right Ventricle	heart
5	chr5:41725600-41747400	Weak transcription	Fetal Kidney	kidney
6	chr5:41726600-41736000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr5:41726600-41736000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:41727200-41735200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr5:41727200-41735800	Weak transcription	Lung	lung
10	chr5:41727200-41738400	Weak transcription	Thymus	Thymus
11	chr5:41727400-41735400	Weak transcription	Hela-S3	cervix
12	chr5:41727400-41751400	Weak transcription	Fetal Brain Female	brain
13	chr5:41727600-41735400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:41727600-41735400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:41727600-41738400	Weak transcription	Gastric	stomach
16	chr5:41727600-41738400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr5:41727800-41738400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr5:41727800-41747200	Weak transcription	NH-A	brain
19	chr5:41727800-41758200	Weak transcription	Esophagus	oesophagus
20	chr5:41728000-41739200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr5:41728200-41738400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr5:41728600-41735200	Weak transcription	Adipose Nuclei	Adipose
23	chr5:41728600-41763800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:41728800-41738400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr5:41728800-41738400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr5:41729000-41736000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr5:41729000-41738400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr5:41729200-41735200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr5:41729200-41736800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:41729200-41737000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:41729200-41738000	Weak transcription	HMEC	breast
32	chr5:41729200-41738400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:41729200-41738400	Weak transcription	Brain Anterior Caudate	brain
34	chr5:41729200-41738400	Weak transcription	NHEK	skin
35	chr5:41729200-41755000	Weak transcription	NHDF-Ad	bronchial
36	chr5:41729400-41735400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:41729400-41736000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr5:41729400-41736800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:41729400-41737000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr5:41729400-41737000	Weak transcription	Fetal Thymus	thymus
41	chr5:41729400-41738600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr5:41729600-41736800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr5:41729600-41737200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr5:41729800-41739000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr5:41729800-41739200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr5:41730000-41738600	Weak transcription	Brain Hippocampus Middle	brain
47	chr5:41730200-41764000	Weak transcription	Spleen	Spleen
48	chr5:41730600-41739200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:41730600-41760800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr5:41730800-41736800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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