Variant report

Variant	rs16940343
Chromosome Location	chr18:13309150-13309151
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10084046	0.91[JPT][hapmap]
rs11080642	1.00[JPT][hapmap]
rs1225	0.87[JPT][hapmap]
rs12955311	0.82[ASN][1000 genomes]
rs12959004	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12959077	0.80[ASN][1000 genomes]
rs12959091	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12969364	0.89[EUR][1000 genomes]
rs16940349	0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1869496	0.84[ASN][1000 genomes]
rs1869497	0.89[GIH][hapmap];0.87[MEX][hapmap]
rs2085049	0.87[JPT][hapmap]
rs2085050	0.91[JPT][hapmap]
rs2187502	0.91[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap]
rs2276392	0.82[JPT][hapmap]
rs2867874	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2867875	0.80[ASN][1000 genomes]
rs4570934	0.91[JPT][hapmap]
rs4570935	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4797761	0.87[JPT][hapmap]
rs6505798	0.82[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs6505802	0.83[ASN][1000 genomes]
rs7226901	0.84[JPT][hapmap]
rs7231366	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs7231701	0.89[ASN][1000 genomes]
rs7234501	0.91[JPT][hapmap]
rs7236152	0.94[JPT][hapmap]
rs7241109	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7241410	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7241438	0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7242024	0.95[JPT][hapmap]
rs7242140	0.95[JPT][hapmap]
rs7242207	0.87[ASN][1000 genomes]
rs7242230	0.87[ASN][1000 genomes]
rs8087505	0.91[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap]
rs8094197	0.91[JPT][hapmap]
rs9303783	0.81[ASN][1000 genomes]
rs930797	0.81[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs930798	0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs930799	0.82[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs949259	0.95[JPT][hapmap]
rs9953274	0.91[JPT][hapmap]
rs9954359	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv2209	chr18:13276410-13316570	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv531246	chr18:13298774-14082028	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16940343	C18orf19	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13285000-13316200	Weak transcription	Aorta	Aorta
2	chr18:13295600-13312600	Weak transcription	Dnd41	blood
3	chr18:13298800-13314600	Weak transcription	Fetal Intestine Small	intestine
4	chr18:13303000-13314400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr18:13303200-13312400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr18:13303200-13314400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr18:13303200-13314600	Weak transcription	Colonic Mucosa	Colon
8	chr18:13303200-13316600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr18:13303200-13318600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr18:13303200-13318600	Weak transcription	Right Atrium	heart
11	chr18:13303400-13314600	Weak transcription	Fetal Lung	lung
12	chr18:13303400-13314600	Weak transcription	Fetal Stomach	stomach
13	chr18:13303600-13318600	Weak transcription	Colon Smooth Muscle	Colon
14	chr18:13304200-13311200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr18:13304400-13313200	Weak transcription	Spleen	Spleen
16	chr18:13304600-13310000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr18:13304600-13315000	Weak transcription	Brain Hippocampus Middle	brain
18	chr18:13305000-13315000	Weak transcription	Brain Anterior Caudate	brain
19	chr18:13306400-13311000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr18:13306600-13309200	Weak transcription	Left Ventricle	heart
21	chr18:13306800-13315800	Weak transcription	Adipose Nuclei	Adipose
22	chr18:13307200-13309200	Enhancers	Fetal Brain Female	brain
23	chr18:13307200-13309400	Enhancers	Fetal Thymus	thymus
24	chr18:13307200-13310200	Enhancers	Primary T cells fromperipheralblood	blood
25	chr18:13307800-13311600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr18:13308000-13309800	Enhancers	Primary T cells from cord blood	blood
27	chr18:13308000-13309800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr18:13308200-13310800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr18:13308200-13310800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr18:13308400-13309600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr18:13308400-13309600	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr18:13308400-13310200	Enhancers	Fetal Heart	heart
33	chr18:13308400-13311800	Genic enhancers	Thymus	Thymus
34	chr18:13308600-13309200	Weak transcription	Pancreas	Pancrea
35	chr18:13308600-13312400	Weak transcription	Liver	Liver
36	chr18:13308600-13314400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr18:13308600-13314600	Weak transcription	Brain Germinal Matrix	brain
38	chr18:13308800-13312400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr18:13308800-13313200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr18:13309000-13310600	Enhancers	Right Ventricle	heart
41	chr18:13309000-13312600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr18:13309000-13313000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr18:13309000-13315800	Weak transcription	Small Intestine	intestine

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