Variant report

Variant	rs13162040
Chromosome Location	chr5:41764302-41764303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:41715717..41717936-chr5:41762141..41764322,2	K562	blood:

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10941559	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11738517	0.94[EUR][1000 genomes]
rs11739106	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11739257	0.99[EUR][1000 genomes]
rs11740524	0.96[EUR][1000 genomes]
rs11740946	1.00[EUR][1000 genomes]
rs11742249	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11744279	1.00[EUR][1000 genomes]
rs11744516	1.00[EUR][1000 genomes]
rs11744623	0.97[EUR][1000 genomes]
rs11746511	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11747881	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11747921	1.00[EUR][1000 genomes]
rs11749008	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11750607	0.89[EUR][1000 genomes]
rs11750760	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11750790	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13153468	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13153837	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13155013	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13155338	0.85[EUR][1000 genomes]
rs13156367	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13163137	1.00[EUR][1000 genomes]
rs13164201	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13165731	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13167578	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13168035	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13169285	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13169977	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13170096	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13176368	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13177937	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13179852	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13180405	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13180475	0.86[EUR][1000 genomes]
rs13182336	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13185973	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13186086	0.85[EUR][1000 genomes]
rs13189403	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1345781	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1389756	0.86[EUR][1000 genomes]
rs1508815	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1508818	0.89[EUR][1000 genomes]
rs16871955	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16871972	0.99[EUR][1000 genomes]
rs16900142	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1876653	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1876654	0.95[EUR][1000 genomes]
rs2081102	0.86[EUR][1000 genomes]
rs33967331	1.00[EUR][1000 genomes]
rs34048302	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34071445	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34193394	0.85[EUR][1000 genomes]
rs34329864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34339137	1.00[EUR][1000 genomes]
rs34369972	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34412181	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34500930	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34569700	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34625465	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34663371	1.00[EUR][1000 genomes]
rs34841703	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34873414	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34898214	0.85[EUR][1000 genomes]
rs35077044	1.00[EUR][1000 genomes]
rs35244816	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35252930	1.00[EUR][1000 genomes]
rs35343042	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35613904	0.97[EUR][1000 genomes]
rs35691805	0.85[EUR][1000 genomes]
rs35748945	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35764180	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35861205	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36005620	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36009913	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36113900	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3926618	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4957430	0.99[EUR][1000 genomes]
rs55817686	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56017638	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60209308	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62360521	0.85[EUR][1000 genomes]
rs62360542	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66820325	0.99[EUR][1000 genomes]
rs67114999	1.00[EUR][1000 genomes]
rs67206815	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67715253	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67869805	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6865448	0.82[AMR][1000 genomes]
rs6866549	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6879341	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6881206	0.85[EUR][1000 genomes]
rs6881873	0.99[EUR][1000 genomes]
rs6883144	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6888816	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6889217	1.00[EUR][1000 genomes]
rs72746918	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72746919	0.99[EUR][1000 genomes]
rs72746957	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7709500	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7712911	0.94[EUR][1000 genomes]
rs7724934	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7725264	0.87[EUR][1000 genomes]
rs951883	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs964267	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9687619	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9763018	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13162040	OXCT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41731400-41800400	Weak transcription	Small Intestine	intestine
2	chr5:41735800-41800400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:41739400-41770800	Weak transcription	Pancreas	Pancrea
4	chr5:41739400-41788800	Weak transcription	Gastric	stomach
5	chr5:41739400-41790200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:41739400-41799600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:41739600-41764600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr5:41739600-41765200	Weak transcription	Lung	lung
9	chr5:41739600-41768000	Weak transcription	Right Ventricle	heart
10	chr5:41739600-41786400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr5:41739600-41794800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:41739800-41770400	Weak transcription	Fetal Stomach	stomach
13	chr5:41747000-41784000	Weak transcription	K562	blood
14	chr5:41747400-41777600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:41747800-41766400	Weak transcription	Brain Angular Gyrus	brain
16	chr5:41748200-41776000	Weak transcription	HUVEC	blood vessel
17	chr5:41748800-41768000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr5:41749200-41764600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:41749200-41786000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr5:41749200-41797800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr5:41751800-41764600	Weak transcription	Fetal Brain Female	brain
22	chr5:41752000-41789400	Weak transcription	Brain Hippocampus Middle	brain
23	chr5:41756200-41813800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr5:41756400-41764800	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr5:41756600-41766400	Strong transcription	Primary T cells from cord blood	blood
26	chr5:41756800-41766400	Strong transcription	Dnd41	blood
27	chr5:41758800-41769800	Weak transcription	Fetal Intestine Small	intestine
28	chr5:41759600-41783400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:41759800-41765600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr5:41759800-41769600	Weak transcription	Fetal Muscle Leg	muscle
31	chr5:41759800-41800400	Weak transcription	Esophagus	oesophagus
32	chr5:41760600-41789400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr5:41761200-41798400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr5:41761600-41772800	Weak transcription	Hela-S3	cervix
35	chr5:41761600-41804600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr5:41761800-41769000	Weak transcription	Thymus	Thymus
37	chr5:41761800-41772800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr5:41761800-41795000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr5:41762000-41765400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr5:41762000-41782800	Weak transcription	Fetal Thymus	thymus
41	chr5:41762000-41799600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr5:41762200-41775800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr5:41762200-41794200	Weak transcription	Adipose Nuclei	Adipose
44	chr5:41762400-41764400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:41762400-41765600	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr5:41762400-41782800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr5:41762400-41794400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:41762600-41764600	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr5:41762600-41765000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr5:41762600-41765000	Enhancers	NHDF-Ad	bronchial

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