Variant report

Variant	rs7241438
Chromosome Location	chr18:13313351-13313352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10084046	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11080642	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11080646	0.84[CHD][hapmap]
rs11662722	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1225	0.83[JPT][hapmap]
rs12456874	0.90[CEU][hapmap]
rs12955311	0.81[ASN][1000 genomes]
rs12959004	0.83[ASN][1000 genomes]
rs12959077	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12959091	1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12961452	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16940343	0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs16940349	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1840267	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1869496	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1869497	1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs1893980	0.83[CEU][hapmap]
rs2085048	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2085049	0.83[JPT][hapmap]
rs2085050	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2187501	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2187502	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2276392	0.90[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs2867874	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2867875	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2867876	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4570934	0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4570935	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4606791	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4797761	0.83[JPT][hapmap]
rs55882226	0.85[EUR][1000 genomes]
rs6505798	0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6505802	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6505803	0.84[ASN][1000 genomes]
rs7226901	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7227361	0.95[CEU][hapmap]
rs7230643	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7231366	0.88[ASW][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7231701	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7234501	0.95[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7234675	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7236152	0.84[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7236934	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7237181	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7237577	0.86[CHD][hapmap];0.82[LWK][hapmap]
rs7241109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7241410	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7242024	1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7242140	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7242207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7242230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8087505	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8094197	0.90[CEU][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs897035	0.90[CEU][hapmap]
rs9303783	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs930797	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs930798	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs930799	0.95[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs949259	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9948620	0.86[MEX][hapmap]
rs9952682	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9952836	0.90[CEU][hapmap];0.95[MEX][hapmap]
rs9953274	0.85[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9954359	0.90[CEU][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs9957621	0.95[CEU][hapmap]
rs9963572	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7241438	TUBB6	cis	cerebellum	SCAN
rs7241438	C18orf19	cis	cerebellum	SCAN
rs7241438	AFG3L2	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13285000-13316200	Weak transcription	Aorta	Aorta
2	chr18:13298800-13314600	Weak transcription	Fetal Intestine Small	intestine
3	chr18:13303000-13314400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr18:13303200-13314400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr18:13303200-13314600	Weak transcription	Colonic Mucosa	Colon
6	chr18:13303200-13316600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr18:13303200-13318600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr18:13303200-13318600	Weak transcription	Right Atrium	heart
9	chr18:13303400-13314600	Weak transcription	Fetal Lung	lung
10	chr18:13303400-13314600	Weak transcription	Fetal Stomach	stomach
11	chr18:13303600-13318600	Weak transcription	Colon Smooth Muscle	Colon
12	chr18:13304600-13315000	Weak transcription	Brain Hippocampus Middle	brain
13	chr18:13305000-13315000	Weak transcription	Brain Anterior Caudate	brain
14	chr18:13306800-13315800	Weak transcription	Adipose Nuclei	Adipose
15	chr18:13308600-13314400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr18:13308600-13314600	Weak transcription	Brain Germinal Matrix	brain
17	chr18:13309000-13315800	Weak transcription	Small Intestine	intestine
18	chr18:13309800-13315800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr18:13309800-13315800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr18:13310200-13316000	Weak transcription	Fetal Heart	heart
21	chr18:13310600-13316400	Weak transcription	Left Ventricle	heart
22	chr18:13310600-13318600	Weak transcription	Right Ventricle	heart
23	chr18:13311800-13314000	Enhancers	Thymus	Thymus
24	chr18:13311800-13315800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr18:13312400-13313600	Strong transcription	Stomach Smooth Muscle	stomach
26	chr18:13312400-13314400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr18:13312400-13314600	Enhancers	Primary hematopoietic stem cells	blood
28	chr18:13312400-13314800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr18:13312400-13315200	Enhancers	Primary T cells from cord blood	blood
30	chr18:13312600-13313400	Strong transcription	Fetal Brain Female	brain
31	chr18:13312600-13313600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr18:13312600-13313800	Enhancers	Dnd41	blood
33	chr18:13312600-13314200	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr18:13312600-13314200	Enhancers	Fetal Thymus	thymus
35	chr18:13312600-13315000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr18:13312600-13315200	Enhancers	Primary T cells fromperipheralblood	blood
37	chr18:13312800-13313600	Flanking Active TSS	Liver	Liver
38	chr18:13312800-13314400	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr18:13312800-13314600	Weak transcription	Esophagus	oesophagus
40	chr18:13313000-13313400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr18:13313000-13313400	Flanking Active TSS	HepG2	liver
42	chr18:13313000-13313600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr18:13313000-13313800	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr18:13313000-13313800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr18:13313000-13314000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr18:13313200-13313400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr18:13313200-13313400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr18:13313200-13313600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr18:13313200-13313600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr18:13313200-13313800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood

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