Variant report

Variant	rs9687619
Chromosome Location	chr5:41862129-41862130
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:40833527..40835162-chr5:41861192..41862978,2	MCF-7	breast:
2	chr5:41856596..41862503-chr5:41900632..41904623,6	K562	blood:
3	chr5:41862125..41865078-chr5:42002913..42005308,2	K562	blood:

Variant related genes	Relation type
ENSG00000145592	Chromatin interaction
ENSG00000205765	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10941559	1.00[CEU][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11738517	0.91[EUR][1000 genomes]
rs11739106	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11739257	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs11740524	0.99[EUR][1000 genomes]
rs11740946	0.97[EUR][1000 genomes]
rs11742249	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11744279	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11744516	0.97[EUR][1000 genomes]
rs11744623	1.00[EUR][1000 genomes]
rs11746511	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11747881	1.00[CEU][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11747921	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11749008	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11750607	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs11750760	0.93[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11750790	0.80[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13153468	1.00[CEU][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13153837	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13155013	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13155338	0.83[EUR][1000 genomes]
rs13156367	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13162040	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13163137	0.97[EUR][1000 genomes]
rs13164201	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13165731	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13167578	0.87[CEU][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13168035	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13169285	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13169977	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13170096	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13176368	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13177937	0.88[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13179852	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13180405	0.88[CEU][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13180475	0.83[EUR][1000 genomes]
rs13182336	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13185973	1.00[CEU][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13186086	0.83[EUR][1000 genomes]
rs13189403	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1345781	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1389756	0.83[EUR][1000 genomes]
rs1508815	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1508818	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs16871955	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16871972	0.99[EUR][1000 genomes]
rs16900142	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1876653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1876654	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2081102	0.83[EUR][1000 genomes]
rs33967331	0.97[EUR][1000 genomes]
rs34048302	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34071445	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34193394	0.83[EUR][1000 genomes]
rs34329864	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34339137	0.97[EUR][1000 genomes]
rs34369972	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34412181	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34500930	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34569700	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34625465	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34663371	0.97[EUR][1000 genomes]
rs34841703	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34873414	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34898214	0.83[EUR][1000 genomes]
rs35077044	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs35244816	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35252930	0.97[EUR][1000 genomes]
rs35343042	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35613904	1.00[EUR][1000 genomes]
rs35691805	0.83[EUR][1000 genomes]
rs35748945	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35764180	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35861205	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36005620	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36009913	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36113900	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3926618	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4957430	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs55817686	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56017638	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60209308	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62360521	0.83[EUR][1000 genomes]
rs62360542	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66820325	0.99[EUR][1000 genomes]
rs67114999	0.97[EUR][1000 genomes]
rs67206815	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67715253	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67869805	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6865448	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6866549	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6879341	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6881206	0.87[EUR][1000 genomes]
rs6881873	0.99[EUR][1000 genomes]
rs6883144	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6888816	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6889217	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs72746918	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72746919	0.96[EUR][1000 genomes]
rs72746957	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7709500	1.00[CEU][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7712911	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7721136	0.82[EUR][1000 genomes]
rs7724934	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7725264	0.80[CEU][hapmap];0.90[EUR][1000 genomes]
rs951883	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs964267	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9763018	0.88[AMR][1000 genomes];0.87[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
rs9687619	OXCT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41832800-41869200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:41836600-41863800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr5:41841800-41869200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:41849000-41862200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr5:41849000-41862600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:41849000-41862800	Strong transcription	Primary B cells from peripheral blood	blood
7	chr5:41849000-41862800	Strong transcription	Fetal Thymus	thymus
8	chr5:41849200-41862400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:41849200-41862800	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr5:41849200-41863600	Strong transcription	Hela-S3	cervix
11	chr5:41849800-41864000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:41849800-41869000	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr5:41850400-41864200	Weak transcription	Brain Angular Gyrus	brain
14	chr5:41850400-41868800	Weak transcription	Fetal Brain Male	brain
15	chr5:41850400-41869000	Weak transcription	Esophagus	oesophagus
16	chr5:41850400-41869000	Weak transcription	Fetal Heart	heart
17	chr5:41850400-41869000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr5:41851000-41869400	Weak transcription	Psoas Muscle	Psoas
19	chr5:41851200-41869000	Weak transcription	Stomach Mucosa	stomach
20	chr5:41852200-41869000	Weak transcription	Brain Germinal Matrix	brain
21	chr5:41852200-41869000	Weak transcription	Gastric	stomach
22	chr5:41852200-41869000	Weak transcription	Right Ventricle	heart
23	chr5:41852200-41869200	Weak transcription	Brain Substantia Nigra	brain
24	chr5:41852400-41869000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr5:41852400-41869400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:41852800-41864000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr5:41852800-41868800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr5:41852800-41868800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr5:41853000-41869000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr5:41853000-41869000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr5:41853000-41869000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr5:41853000-41869000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr5:41853200-41869200	Weak transcription	Lung	lung
34	chr5:41853200-41869400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr5:41853400-41869000	Weak transcription	Fetal Intestine Small	intestine
36	chr5:41853400-41869000	Weak transcription	Fetal Stomach	stomach
37	chr5:41853600-41869000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr5:41854000-41863200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:41854000-41864200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:41854200-41863600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:41854200-41869200	Weak transcription	Small Intestine	intestine
42	chr5:41854200-41869200	Weak transcription	HSMM	muscle
43	chr5:41855400-41869000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr5:41855800-41868800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr5:41856200-41869000	Weak transcription	Aorta	Aorta
46	chr5:41856400-41869200	Weak transcription	Fetal Intestine Large	intestine
47	chr5:41856600-41869400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr5:41856800-41869000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr5:41856800-41869000	Weak transcription	Thymus	Thymus
50	chr5:41857000-41868800	Weak transcription	Colon Smooth Muscle	Colon

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