Variant report

Variant	rs60209308
Chromosome Location	chr5:41797376-41797377
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr5:41797177-41797831	MCF10A-Er-Src	breast:	n/a	chr5:41797189-41797197

Variant related genes	Relation type
OXCT1	TF binding region

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

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

rs_ID	r²[population]
rs10941559	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11738517	0.94[EUR][1000 genomes]
rs11739106	0.96[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	0.87[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	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11747881	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11747921	1.00[EUR][1000 genomes]
rs11749008	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11750607	0.89[EUR][1000 genomes]
rs11750760	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11750790	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13153468	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13153837	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13155013	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13155338	0.85[EUR][1000 genomes]
rs13156367	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13162040	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13163137	1.00[EUR][1000 genomes]
rs13164201	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13165731	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13167578	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13168035	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13169285	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13169977	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13170096	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13176368	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13177937	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13179852	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13180405	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13180475	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13182336	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13185973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13186086	0.85[EUR][1000 genomes]
rs13189403	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1345781	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1389756	0.86[EUR][1000 genomes]
rs1508815	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1508818	0.89[EUR][1000 genomes]
rs16871955	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16871972	0.99[EUR][1000 genomes]
rs16900142	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1876653	0.96[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	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34071445	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34193394	0.85[EUR][1000 genomes]
rs34329864	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34339137	1.00[EUR][1000 genomes]
rs34369972	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34412181	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34500930	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34569700	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34625465	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34663371	1.00[EUR][1000 genomes]
rs34841703	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34873414	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34898214	0.85[EUR][1000 genomes]
rs35077044	1.00[EUR][1000 genomes]
rs35244816	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35252930	1.00[EUR][1000 genomes]
rs35343042	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35613904	0.97[EUR][1000 genomes]
rs35691805	0.85[EUR][1000 genomes]
rs35748945	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35764180	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35861205	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36005620	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36009913	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36113900	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3926618	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4957430	0.99[EUR][1000 genomes]
rs55817686	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56017638	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62360521	0.85[EUR][1000 genomes]
rs62360542	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66820325	0.99[EUR][1000 genomes]
rs67114999	1.00[EUR][1000 genomes]
rs67206815	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67715253	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67869805	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6865448	0.85[AMR][1000 genomes]
rs6866549	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6879341	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6881206	0.85[EUR][1000 genomes]
rs6881873	0.99[EUR][1000 genomes]
rs6883144	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6888816	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6889217	1.00[EUR][1000 genomes]
rs72746918	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72746919	0.99[EUR][1000 genomes]
rs72746957	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7709500	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7712911	0.94[EUR][1000 genomes]
rs7724934	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7725264	0.87[EUR][1000 genomes]
rs951883	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs964267	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9687619	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9763018	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60209308	OXCT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

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	chr5:41739400-41799600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:41749200-41797800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr5:41756200-41813800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:41759800-41800400	Weak transcription	Esophagus	oesophagus
7	chr5:41761200-41798400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr5:41761600-41804600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr5:41762000-41799600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr5:41776000-41798200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr5:41778200-41838200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:41780000-41800200	Weak transcription	Fetal Intestine Large	intestine
13	chr5:41785800-41800000	Weak transcription	Fetal Brain Male	brain
14	chr5:41788600-41800000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:41789600-41808200	Weak transcription	Fetal Intestine Small	intestine
16	chr5:41790200-41801400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:41790200-41801600	Strong transcription	Primary T cells from cord blood	blood
18	chr5:41790400-41814000	Weak transcription	Psoas Muscle	Psoas
19	chr5:41791000-41801200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr5:41791600-41807600	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr5:41792200-41801000	Strong transcription	Primary B cells from cord blood	blood
22	chr5:41792200-41801400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr5:41792400-41799000	Strong transcription	Fetal Thymus	thymus
24	chr5:41792600-41798800	Strong transcription	GM12878-XiMat	blood
25	chr5:41792600-41800400	Weak transcription	Gastric	stomach
26	chr5:41793000-41800200	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr5:41793400-41800400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr5:41793400-41801200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr5:41793400-41810400	Weak transcription	Spleen	Spleen
30	chr5:41794400-41799000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:41795200-41800000	Weak transcription	Adipose Nuclei	Adipose
32	chr5:41795200-41800400	Weak transcription	Brain Hippocampus Middle	brain
33	chr5:41795200-41800400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr5:41795200-41805800	Weak transcription	Brain Angular Gyrus	brain
35	chr5:41795400-41798000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:41795400-41800000	Weak transcription	Brain Germinal Matrix	brain
37	chr5:41795400-41800200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr5:41795400-41800400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr5:41795400-41800400	Weak transcription	Right Ventricle	heart
40	chr5:41795400-41809400	Weak transcription	Fetal Kidney	kidney
41	chr5:41795400-41809800	Weak transcription	Brain Anterior Caudate	brain
42	chr5:41795400-41813000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr5:41795400-41816200	Weak transcription	Colon Smooth Muscle	Colon
44	chr5:41795400-41835800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:41795600-41798000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr5:41795600-41798400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr5:41795600-41799400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr5:41795600-41799600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr5:41795600-41799800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr5:41795600-41800000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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