Variant report

Variant	rs35748945
Chromosome Location	chr5:41909115-41909116
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:41903420..41907025-chr5:41907482..41911451,8	MCF-7	breast:
2	chr5:41908677..41910534-chr5:41913765..41916723,2	MCF-7	breast:
3	chr5:41903099..41906960-chr5:41907853..41912550,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205765	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10941559	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11738517	0.83[EUR][1000 genomes]
rs11739106	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11739257	0.91[EUR][1000 genomes]
rs11740524	0.92[EUR][1000 genomes]
rs11740946	0.89[EUR][1000 genomes]
rs11742249	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11744279	0.89[EUR][1000 genomes]
rs11744516	0.89[EUR][1000 genomes]
rs11744623	0.92[EUR][1000 genomes]
rs11746511	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11747881	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11747921	0.89[EUR][1000 genomes]
rs11749008	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11750607	1.00[EUR][1000 genomes]
rs11750760	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11750790	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13153468	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13153837	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13155013	0.85[AMR][1000 genomes]
rs13156367	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13162040	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13163137	0.89[EUR][1000 genomes]
rs13164201	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13165731	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13167578	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13168035	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13169285	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13169977	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13170096	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13176368	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13177937	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13179852	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13180405	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13182336	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13185973	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13189403	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1345781	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1508815	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1508818	1.00[EUR][1000 genomes]
rs16871955	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16871972	0.91[EUR][1000 genomes]
rs16900142	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1876653	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1876654	0.90[EUR][1000 genomes]
rs33967331	0.89[EUR][1000 genomes]
rs34048302	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34071445	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34329864	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34339137	0.89[EUR][1000 genomes]
rs34369972	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34412181	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34500930	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34569700	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34625465	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34663371	0.89[EUR][1000 genomes]
rs34841703	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34873414	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35077044	0.89[EUR][1000 genomes]
rs35244816	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35252930	0.89[EUR][1000 genomes]
rs35343042	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35613904	0.92[EUR][1000 genomes]
rs35764180	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35861205	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36005620	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36009913	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36113900	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3926618	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4957430	0.91[EUR][1000 genomes]
rs55817686	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56017638	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60209308	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62360542	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66820325	0.91[EUR][1000 genomes]
rs67114999	0.89[EUR][1000 genomes]
rs67206815	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67715253	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67869805	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6865448	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6866549	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6879341	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6881206	0.95[EUR][1000 genomes]
rs6881873	0.91[EUR][1000 genomes]
rs6883144	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6888816	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6889217	0.89[EUR][1000 genomes]
rs72746918	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72746919	0.88[EUR][1000 genomes]
rs72746957	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7709500	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7712911	0.89[EUR][1000 genomes]
rs7721136	0.89[EUR][1000 genomes]
rs7724934	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7725264	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs951883	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs964267	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9687619	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9763018	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv830273	chr5:41867296-42066070	Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
4	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
5	nsv327668	chr5:41901383-41909830	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35748945	OXCT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41905000-41924800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:41905200-41912600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:41905200-41912600	Weak transcription	Fetal Stomach	stomach
4	chr5:41905200-41915400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:41905200-41918200	Weak transcription	Aorta	Aorta
6	chr5:41905200-41925000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:41905400-41910200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:41905600-41910000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr5:41905600-41910200	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:41905600-41911200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:41905600-41912600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr5:41905600-41912600	Weak transcription	Lung	lung
13	chr5:41905600-41912600	Weak transcription	Thymus	Thymus
14	chr5:41905600-41912800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr5:41905600-41921000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr5:41905600-41924600	Weak transcription	Small Intestine	intestine
17	chr5:41905800-41910200	Weak transcription	Esophagus	oesophagus
18	chr5:41905800-41910200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr5:41905800-41911400	Weak transcription	Brain Germinal Matrix	brain
20	chr5:41905800-41911400	Weak transcription	Fetal Brain Male	brain
21	chr5:41905800-41912200	Weak transcription	NHEK	skin
22	chr5:41905800-41912600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:41905800-41912600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:41905800-41912600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr5:41905800-41912600	Weak transcription	Pancreas	Pancrea
26	chr5:41905800-41912800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr5:41905800-41918200	Weak transcription	Psoas Muscle	Psoas
28	chr5:41905800-41918200	Weak transcription	Spleen	Spleen
29	chr5:41905800-41922200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr5:41905800-41923800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:41905800-41924400	Weak transcription	Stomach Mucosa	stomach
32	chr5:41905800-41925000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr5:41905800-41925000	Weak transcription	Gastric	stomach
34	chr5:41906000-41910200	Weak transcription	A549	lung
35	chr5:41906200-41921200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr5:41906400-41916400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:41906400-41920600	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr5:41906400-41921000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr5:41906400-41922200	Strong transcription	Fetal Muscle Trunk	muscle
40	chr5:41906600-41909200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:41906600-41918200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr5:41906800-41924600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr5:41907000-41910200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:41907000-41910200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr5:41907000-41922200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr5:41907000-41923600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr5:41907200-41912800	Weak transcription	Right Ventricle	heart
48	chr5:41907200-41914400	Weak transcription	Fetal Intestine Small	intestine
49	chr5:41907200-41915600	Strong transcription	K562	blood
50	chr5:41907200-41922400	Strong transcription	Liver	Liver

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