Variant report

Variant	rs11746511
Chromosome Location	chr5:41849665-41849666
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10051536	1.00[CHB][hapmap]
rs10077481	1.00[CHB][hapmap]
rs10941559	0.84[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11738517	0.92[EUR][1000 genomes]
rs11739106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11739257	0.84[CEU][hapmap];1.00[EUR][1000 genomes]
rs11740524	0.98[EUR][1000 genomes]
rs11740946	0.99[EUR][1000 genomes]
rs11742249	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11744279	0.82[CEU][hapmap];0.99[EUR][1000 genomes]
rs11744516	0.99[EUR][1000 genomes]
rs11744623	0.99[EUR][1000 genomes]
rs11747881	0.92[ASW][hapmap];0.84[CEU][hapmap];1.00[GIH][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11747921	0.99[EUR][1000 genomes]
rs11749008	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11750607	0.82[GIH][hapmap];0.91[EUR][1000 genomes]
rs11750760	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11750790	0.85[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12186512	0.89[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs13153468	0.92[ASW][hapmap];0.84[CEU][hapmap];1.00[GIH][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13153837	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13155013	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13155338	0.84[EUR][1000 genomes]
rs13156367	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13162040	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13163137	0.99[EUR][1000 genomes]
rs13164201	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13165731	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13167578	0.84[MKK][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13168035	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13169285	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13169977	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13170096	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13176368	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13177937	0.92[ASW][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13179852	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13180405	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13180475	0.85[EUR][1000 genomes]
rs13182336	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13182886	1.00[CHB][hapmap]
rs13185973	0.83[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13186086	0.84[EUR][1000 genomes]
rs13189403	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1345781	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1389756	0.85[EUR][1000 genomes]
rs1508815	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1508818	0.91[EUR][1000 genomes]
rs16871955	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16871972	1.00[EUR][1000 genomes]
rs16900142	0.84[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1876653	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1876654	0.92[ASW][hapmap];0.81[CEU][hapmap];0.96[EUR][1000 genomes]
rs2081102	0.85[EUR][1000 genomes]
rs33967331	0.99[EUR][1000 genomes]
rs34048302	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34071445	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34193394	0.84[EUR][1000 genomes]
rs34329864	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34339137	0.99[EUR][1000 genomes]
rs34369972	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34412181	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34500930	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34569700	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34625465	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34663371	0.99[EUR][1000 genomes]
rs34841703	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34873414	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34898214	0.84[EUR][1000 genomes]
rs35077044	0.84[CEU][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes]
rs35244816	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35252930	0.99[EUR][1000 genomes]
rs35343042	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35613904	0.99[EUR][1000 genomes]
rs35691805	0.84[EUR][1000 genomes]
rs35748945	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35764180	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35861205	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs36005620	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs36009913	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36113900	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3926618	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4957430	0.89[CEU][hapmap];0.94[TSI][hapmap];1.00[EUR][1000 genomes]
rs55817686	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56017638	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60209308	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62360521	0.84[EUR][1000 genomes]
rs62360542	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66820325	1.00[EUR][1000 genomes]
rs67114999	0.99[EUR][1000 genomes]
rs67206815	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67715253	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67869805	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6865448	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6866549	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6879341	0.92[ASW][hapmap];0.84[CEU][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6881206	0.86[EUR][1000 genomes]
rs6881873	1.00[EUR][1000 genomes]
rs6883144	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6888816	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6889217	0.84[CEU][hapmap];0.99[EUR][1000 genomes]
rs72746918	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72746919	0.97[EUR][1000 genomes]
rs72746957	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7709500	0.92[ASW][hapmap];0.84[CEU][hapmap];1.00[GIH][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7712911	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs7721136	0.81[EUR][1000 genomes]
rs7724934	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7725264	0.89[EUR][1000 genomes]
rs951883	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs964267	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9687619	0.83[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9763018	0.88[AMR][1000 genomes];0.88[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
rs11746511	OXCT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41818400-41852000	Weak transcription	Small Intestine	intestine
2	chr5:41819200-41852800	Weak transcription	Pancreas	Pancrea
3	chr5:41824600-41859400	Weak transcription	Spleen	Spleen
4	chr5:41827800-41849800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:41829400-41851000	Weak transcription	Fetal Intestine Small	intestine
6	chr5:41830800-41849800	Weak transcription	Gastric	stomach
7	chr5:41831200-41854400	Weak transcription	Colonic Mucosa	Colon
8	chr5:41832800-41850000	Weak transcription	Esophagus	oesophagus
9	chr5:41832800-41869200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:41836000-41857200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr5:41836600-41863800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr5:41837000-41850000	Weak transcription	Brain Angular Gyrus	brain
13	chr5:41837200-41858600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:41839000-41851000	Weak transcription	Lung	lung
15	chr5:41839200-41849800	Weak transcription	Fetal Stomach	stomach
16	chr5:41839200-41850200	Weak transcription	Fetal Intestine Large	intestine
17	chr5:41841600-41849800	Weak transcription	Aorta	Aorta
18	chr5:41841800-41849800	Weak transcription	Right Ventricle	heart
19	chr5:41841800-41869200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:41843800-41855600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr5:41845400-41849800	Weak transcription	Left Ventricle	heart
22	chr5:41849000-41849800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:41849000-41849800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:41849000-41853000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:41849000-41853800	Strong transcription	NHDF-Ad	bronchial
26	chr5:41849000-41855200	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:41849000-41856000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr5:41849000-41856200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr5:41849000-41856400	Strong transcription	Adipose Nuclei	Adipose
30	chr5:41849000-41856600	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr5:41849000-41856600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr5:41849000-41857000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr5:41849000-41857000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:41849000-41857200	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr5:41849000-41857200	Strong transcription	K562	blood
36	chr5:41849000-41857800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:41849000-41862200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:41849000-41862600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr5:41849000-41862800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr5:41849000-41862800	Strong transcription	Fetal Thymus	thymus
41	chr5:41849200-41849800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
42	chr5:41849200-41849800	Strong transcription	Rectal Smooth Muscle	rectum
43	chr5:41849200-41850200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr5:41849200-41850200	ZNF genes & repeats	GM12878-XiMat	blood
45	chr5:41849200-41850400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:41849200-41850400	Strong transcription	Fetal Brain Male	brain
47	chr5:41849200-41850400	Strong transcription	Fetal Heart	heart
48	chr5:41849200-41850400	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr5:41849200-41850400	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr5:41849200-41850400	Strong transcription	NHLF	lung

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