Variant report

Variant	rs6889217
Chromosome Location	chr5:41837149-41837150
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:41837142..41840023-chr5:41841015..41842990,3	K562	blood:

Variant related genes	Relation type
ENSG00000083720	Chromatin interaction

Extended variants
information (count: 149 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10045473	1.00[JPT][hapmap]
rs10059424	1.00[JPT][hapmap]
rs10060170	1.00[JPT][hapmap]
rs10062703	1.00[JPT][hapmap]
rs10064298	1.00[JPT][hapmap]
rs10064380	1.00[JPT][hapmap]
rs10069638	1.00[JPT][hapmap]
rs1006996	1.00[JPT][hapmap]
rs10070201	1.00[JPT][hapmap]
rs10075064	1.00[JPT][hapmap]
rs10077481	1.00[JPT][hapmap]
rs10472357	1.00[JPT][hapmap]
rs10941557	1.00[JPT][hapmap]
rs10941559	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1118104	1.00[JPT][hapmap]
rs11738517	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11739106	0.99[EUR][1000 genomes]
rs11739257	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11740524	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11740946	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11742249	0.87[EUR][1000 genomes]
rs11744279	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11744516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11744623	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11745373	1.00[JPT][hapmap]
rs11746511	0.99[EUR][1000 genomes]
rs11747881	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11747921	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11749008	0.98[EUR][1000 genomes]
rs11750607	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs11750760	0.93[CEU][hapmap];1.00[EUR][1000 genomes]
rs11750790	0.82[CEU][hapmap];1.00[EUR][1000 genomes]
rs13153468	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13153837	0.99[EUR][1000 genomes]
rs13155013	0.86[EUR][1000 genomes]
rs13155338	0.85[EUR][1000 genomes]
rs13156367	0.87[EUR][1000 genomes]
rs13162040	1.00[EUR][1000 genomes]
rs13163137	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13164201	0.99[EUR][1000 genomes]
rs13165731	0.98[EUR][1000 genomes]
rs13167578	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs13168035	1.00[EUR][1000 genomes]
rs13169285	0.93[EUR][1000 genomes]
rs13169977	1.00[EUR][1000 genomes]
rs13170096	0.90[EUR][1000 genomes]
rs13176368	1.00[EUR][1000 genomes]
rs13177937	0.89[CEU][hapmap];1.00[EUR][1000 genomes]
rs13179852	1.00[EUR][1000 genomes]
rs13180405	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs13180475	0.86[EUR][1000 genomes]
rs13182336	1.00[EUR][1000 genomes]
rs13185973	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13186086	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs13189403	0.95[EUR][1000 genomes]
rs13360001	1.00[JPT][hapmap]
rs1345781	0.95[EUR][1000 genomes]
rs1355089	1.00[JPT][hapmap]
rs1389756	0.86[EUR][1000 genomes]
rs1508815	1.00[EUR][1000 genomes]
rs1508816	1.00[JPT][hapmap]
rs1508818	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs16871955	1.00[EUR][1000 genomes]
rs16871972	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16900142	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1876653	0.97[EUR][1000 genomes]
rs1876654	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2081102	0.86[EUR][1000 genomes]
rs2231910	1.00[JPT][hapmap]
rs277414	1.00[JPT][hapmap]
rs277416	1.00[JPT][hapmap]
rs33967331	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34048302	0.93[EUR][1000 genomes]
rs34071445	1.00[EUR][1000 genomes]
rs34193394	0.85[EUR][1000 genomes]
rs34329864	1.00[EUR][1000 genomes]
rs34339137	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34369972	1.00[EUR][1000 genomes]
rs34412181	0.98[EUR][1000 genomes]
rs34500930	1.00[EUR][1000 genomes]
rs34569700	1.00[EUR][1000 genomes]
rs34625465	1.00[EUR][1000 genomes]
rs34663371	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34841703	1.00[EUR][1000 genomes]
rs34873414	1.00[EUR][1000 genomes]
rs34898214	0.85[EUR][1000 genomes]
rs35077044	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35244816	0.87[EUR][1000 genomes]
rs35252930	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35343042	0.99[EUR][1000 genomes]
rs35613904	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35691805	0.85[EUR][1000 genomes]
rs35748945	0.89[EUR][1000 genomes]
rs35764180	0.99[EUR][1000 genomes]
rs35861205	1.00[EUR][1000 genomes]
rs36005620	1.00[EUR][1000 genomes]
rs36009913	0.87[EUR][1000 genomes]
rs36113900	1.00[EUR][1000 genomes]
rs3926618	0.97[EUR][1000 genomes]
rs4957171	1.00[JPT][hapmap]
rs4957173	1.00[JPT][hapmap]
rs4957174	1.00[JPT][hapmap]
rs4957175	1.00[JPT][hapmap]
rs4957176	1.00[JPT][hapmap]
rs4957177	1.00[JPT][hapmap]
rs4957422	1.00[JPT][hapmap]
rs4957423	1.00[JPT][hapmap]
rs4957429	1.00[JPT][hapmap]
rs4957430	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4957431	1.00[JPT][hapmap]
rs4957432	1.00[JPT][hapmap]
rs4957434	1.00[JPT][hapmap]
rs4957435	1.00[JPT][hapmap]
rs4957436	1.00[JPT][hapmap]
rs4957437	1.00[JPT][hapmap]
rs4957438	1.00[JPT][hapmap]
rs55817686	0.99[EUR][1000 genomes]
rs56017638	1.00[EUR][1000 genomes]
rs60209308	1.00[EUR][1000 genomes]
rs62360521	0.85[EUR][1000 genomes]
rs62360542	0.94[EUR][1000 genomes]
rs626907	1.00[JPT][hapmap]
rs6451582	1.00[JPT][hapmap]
rs66820325	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67114999	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67206815	0.99[EUR][1000 genomes]
rs67715253	0.99[EUR][1000 genomes]
rs67869805	0.96[EUR][1000 genomes]
rs6866549	1.00[EUR][1000 genomes]
rs6879341	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6881206	0.85[EUR][1000 genomes]
rs6881873	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6883144	1.00[EUR][1000 genomes]
rs6888816	1.00[EUR][1000 genomes]
rs72746918	0.99[EUR][1000 genomes]
rs72746919	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72746957	1.00[EUR][1000 genomes]
rs7709500	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7712911	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7724934	0.99[EUR][1000 genomes]
rs7725264	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs7728482	1.00[JPT][hapmap]
rs951883	1.00[EUR][1000 genomes]
rs964267	1.00[EUR][1000 genomes]
rs9687619	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs9763018	0.89[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6889217	OXCT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41778200-41838200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:41800800-41838600	Weak transcription	Fetal Stomach	stomach
3	chr5:41801000-41849200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:41801200-41849200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:41801200-41849200	Weak transcription	Fetal Brain Male	brain
6	chr5:41814000-41842200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr5:41816200-41838600	Weak transcription	NHEK	skin
8	chr5:41818400-41852000	Weak transcription	Small Intestine	intestine
9	chr5:41819200-41852800	Weak transcription	Pancreas	Pancrea
10	chr5:41822600-41849200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:41824600-41859400	Weak transcription	Spleen	Spleen
12	chr5:41825800-41849200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr5:41827800-41849800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:41828600-41849200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr5:41828800-41849000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr5:41829000-41838800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:41829400-41851000	Weak transcription	Fetal Intestine Small	intestine
18	chr5:41830000-41843400	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr5:41830800-41849200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr5:41830800-41849800	Weak transcription	Gastric	stomach
21	chr5:41831200-41838200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:41831200-41849200	Weak transcription	Brain Germinal Matrix	brain
23	chr5:41831200-41854400	Weak transcription	Colonic Mucosa	Colon
24	chr5:41831400-41849200	Weak transcription	Placenta	Placenta
25	chr5:41831800-41838400	Weak transcription	GM12878-XiMat	blood
26	chr5:41832200-41849200	Weak transcription	Fetal Kidney	kidney
27	chr5:41832400-41842400	Weak transcription	Fetal Lung	lung
28	chr5:41832400-41842600	Weak transcription	K562	blood
29	chr5:41832600-41838000	Weak transcription	Adipose Nuclei	Adipose
30	chr5:41832600-41838200	Weak transcription	Fetal Brain Female	brain
31	chr5:41832600-41838800	Weak transcription	Lung	lung
32	chr5:41832800-41838000	Weak transcription	Fetal Intestine Large	intestine
33	chr5:41832800-41838800	Weak transcription	Thymus	Thymus
34	chr5:41832800-41849200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr5:41832800-41850000	Weak transcription	Esophagus	oesophagus
36	chr5:41832800-41869200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr5:41833400-41838400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr5:41833400-41849200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr5:41833600-41838800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr5:41833800-41839000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr5:41834000-41838000	Weak transcription	Fetal Thymus	thymus
42	chr5:41834000-41849200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr5:41834200-41838200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr5:41834200-41839600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr5:41834400-41837400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr5:41834600-41838000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:41834600-41849200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr5:41835000-41838200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr5:41835200-41838000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:41835400-41837600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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