Variant report

Variant	rs16900142
Chromosome Location	chr5:41868410-41868411
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:41866741..41868541-chr5:42502813..42504504,2	K562	blood:
2	chr5:41865404..41878163-chr5:41900217..41908471,28	K562	blood:
3	chr5:41866693..41874585-chr5:41920680..41930326,14	K562	blood:
4	chr5:41867500..41871930-chr5:41901815..41908844,17	K562	blood:
5	chr5:41866734..41868498-chr5:41868516..41871487,2	MCF-7	breast:
6	chr5:41866709..41868950-chr5:41930527..41932665,2	K562	blood:
7	chr5:41864208..41872390-chr5:41920936..41926995,11	K562	blood:
8	chr5:41864530..41869583-chr5:41903151..41906093,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000248668	Chromatin interaction
ENSG00000151876	Chromatin interaction
ENSG00000083720	Chromatin interaction
ENSG00000205765	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10941559	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11738517	0.91[EUR][1000 genomes]
rs11739106	0.96[AFR][1000 genomes];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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11747881	1.00[CEU][hapmap];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	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs11750760	0.93[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11750790	0.82[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12186512	1.00[YRI][hapmap]
rs13153468	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13153837	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	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13165731	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13167578	0.88[CEU][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	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13176368	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13177937	0.89[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13179852	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13180405	0.89[CEU][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13180475	0.83[EUR][1000 genomes]
rs13182336	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13185973	1.00[CEU][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	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1508818	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs16871955	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16871972	0.99[EUR][1000 genomes]
rs1876653	0.81[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]
rs34329864	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34339137	0.97[EUR][1000 genomes]
rs34369972	0.80[AFR][1000 genomes];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	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34873414	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35077044	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs35244816	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	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36113900	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3926618	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]
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	1.00[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];0.91[YRI][hapmap];0.84[AFR][1000 genomes];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	0.84[AFR][1000 genomes];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];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	0.82[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]
rs9687619	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9763018	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16900142	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	chr5:41841800-41869200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:41849800-41869000	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr5:41850400-41868800	Weak transcription	Fetal Brain Male	brain
5	chr5:41850400-41869000	Weak transcription	Esophagus	oesophagus
6	chr5:41850400-41869000	Weak transcription	Fetal Heart	heart
7	chr5:41850400-41869000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr5:41851000-41869400	Weak transcription	Psoas Muscle	Psoas
9	chr5:41851200-41869000	Weak transcription	Stomach Mucosa	stomach
10	chr5:41852200-41869000	Weak transcription	Brain Germinal Matrix	brain
11	chr5:41852200-41869000	Weak transcription	Gastric	stomach
12	chr5:41852200-41869000	Weak transcription	Right Ventricle	heart
13	chr5:41852200-41869200	Weak transcription	Brain Substantia Nigra	brain
14	chr5:41852400-41869000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr5:41852400-41869400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:41852800-41868800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:41852800-41868800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:41853000-41869000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr5:41853000-41869000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:41853000-41869000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr5:41853000-41869000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr5:41853200-41869200	Weak transcription	Lung	lung
23	chr5:41853200-41869400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:41853400-41869000	Weak transcription	Fetal Intestine Small	intestine
25	chr5:41853400-41869000	Weak transcription	Fetal Stomach	stomach
26	chr5:41853600-41869000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr5:41854200-41869200	Weak transcription	Small Intestine	intestine
28	chr5:41854200-41869200	Weak transcription	HSMM	muscle
29	chr5:41855400-41869000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr5:41855800-41868800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr5:41856200-41869000	Weak transcription	Aorta	Aorta
32	chr5:41856400-41869200	Weak transcription	Fetal Intestine Large	intestine
33	chr5:41856600-41869400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:41856800-41869000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr5:41856800-41869000	Weak transcription	Thymus	Thymus
36	chr5:41857000-41868800	Weak transcription	Colon Smooth Muscle	Colon
37	chr5:41860600-41868800	Weak transcription	Fetal Lung	lung
38	chr5:41861400-41869000	Weak transcription	Fetal Kidney	kidney
39	chr5:41861600-41869200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:41861800-41868800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr5:41861800-41869000	Weak transcription	Brain Anterior Caudate	brain
42	chr5:41861800-41869000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr5:41862000-41868800	Weak transcription	Adipose Nuclei	Adipose
44	chr5:41862000-41868800	Weak transcription	HMEC	breast
45	chr5:41862000-41869000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr5:41862000-41869000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr5:41862000-41869000	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr5:41862000-41869200	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr5:41862200-41869000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr5:41862200-41869000	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links