Variant report

Variant	rs3926618
Chromosome Location	chr5:41849139-41849140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10941559	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11738517	0.92[EUR][1000 genomes]
rs11739106	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11739257	0.99[EUR][1000 genomes]
rs11740524	0.96[EUR][1000 genomes]
rs11740946	0.97[EUR][1000 genomes]
rs11742249	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11744279	0.97[EUR][1000 genomes]
rs11744516	0.97[EUR][1000 genomes]
rs11744623	0.97[EUR][1000 genomes]
rs11746511	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11747881	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11747921	0.97[EUR][1000 genomes]
rs11749008	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11750607	0.89[EUR][1000 genomes]
rs11750760	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11750790	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13153468	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13153837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13155013	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13155338	0.82[EUR][1000 genomes]
rs13156367	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13162040	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13163137	0.97[EUR][1000 genomes]
rs13164201	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13165731	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13167578	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13168035	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13169285	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13169977	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13170096	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13176368	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13177937	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13179852	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13180405	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13180475	0.83[EUR][1000 genomes]
rs13182336	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13185973	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13186086	0.82[EUR][1000 genomes]
rs13189403	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1345781	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1389756	0.83[EUR][1000 genomes]
rs1508815	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1508818	0.89[EUR][1000 genomes]
rs16871955	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16871972	0.99[EUR][1000 genomes]
rs16900142	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1876653	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1876654	0.95[EUR][1000 genomes]
rs2081102	0.83[EUR][1000 genomes]
rs33967331	0.97[EUR][1000 genomes]
rs34048302	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34071445	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34193394	0.82[EUR][1000 genomes]
rs34329864	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34339137	0.97[EUR][1000 genomes]
rs34369972	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34412181	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34500930	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34569700	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34625465	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34663371	0.97[EUR][1000 genomes]
rs34841703	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34873414	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34898214	0.82[EUR][1000 genomes]
rs35077044	0.97[EUR][1000 genomes]
rs35244816	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35252930	0.97[EUR][1000 genomes]
rs35343042	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35613904	0.97[EUR][1000 genomes]
rs35691805	0.82[EUR][1000 genomes]
rs35748945	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35764180	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35861205	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36005620	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36009913	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36113900	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4957430	0.99[EUR][1000 genomes]
rs55817686	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56017638	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60209308	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62360521	0.82[EUR][1000 genomes]
rs62360542	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66820325	0.99[EUR][1000 genomes]
rs67114999	0.97[EUR][1000 genomes]
rs67206815	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67715253	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67869805	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6865448	0.89[AMR][1000 genomes]
rs6866549	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6879341	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6881206	0.84[EUR][1000 genomes]
rs6881873	0.99[EUR][1000 genomes]
rs6883144	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6888816	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6889217	0.97[EUR][1000 genomes]
rs72746918	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72746919	0.96[EUR][1000 genomes]
rs72746957	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7709500	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7712911	0.94[EUR][1000 genomes]
rs7724934	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7725264	0.87[EUR][1000 genomes]
rs951883	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs964267	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9687619	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9763018	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv2762518	chr5:41780210-41935113	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	108 gene(s)	inside rSNPs	diseases
3	nsv830272	chr5:41833365-41986167	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
4	nsv4811	chr5:41844522-41887353	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3926618	OXCT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41801000-41849200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:41801200-41849200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr5:41801200-41849200	Weak transcription	Fetal Brain Male	brain
4	chr5:41818400-41852000	Weak transcription	Small Intestine	intestine
5	chr5:41819200-41852800	Weak transcription	Pancreas	Pancrea
6	chr5:41822600-41849200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:41824600-41859400	Weak transcription	Spleen	Spleen
8	chr5:41825800-41849200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr5:41827800-41849800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:41828600-41849200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr5:41829400-41851000	Weak transcription	Fetal Intestine Small	intestine
12	chr5:41830800-41849200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr5:41830800-41849800	Weak transcription	Gastric	stomach
14	chr5:41831200-41849200	Weak transcription	Brain Germinal Matrix	brain
15	chr5:41831200-41854400	Weak transcription	Colonic Mucosa	Colon
16	chr5:41831400-41849200	Weak transcription	Placenta	Placenta
17	chr5:41832200-41849200	Weak transcription	Fetal Kidney	kidney
18	chr5:41832800-41849200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr5:41832800-41850000	Weak transcription	Esophagus	oesophagus
20	chr5:41832800-41869200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:41833400-41849200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr5:41834000-41849200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr5:41834600-41849200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr5:41836000-41857200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr5:41836200-41849200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:41836400-41849200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:41836400-41849200	Weak transcription	Brain Anterior Caudate	brain
28	chr5:41836400-41849200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr5:41836400-41849200	Weak transcription	Brain Substantia Nigra	brain
30	chr5:41836400-41849200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr5:41836400-41849200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr5:41836400-41849400	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:41836600-41849200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:41836600-41849200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:41836600-41849200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:41836600-41849200	Weak transcription	Ovary	ovary
37	chr5:41836600-41849200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr5:41836600-41849200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr5:41836600-41849200	Weak transcription	Osteobl	bone
40	chr5:41836600-41849400	Weak transcription	HSMM	muscle
41	chr5:41836600-41863800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr5:41837000-41849200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr5:41837000-41849200	Weak transcription	Fetal Heart	heart
44	chr5:41837000-41849200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr5:41837000-41850000	Weak transcription	Brain Angular Gyrus	brain
46	chr5:41837200-41858600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr5:41837600-41849200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:41837800-41849200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr5:41839000-41849200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr5:41839000-41851000	Weak transcription	Lung	lung

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