Variant report

Variant	rs11080646
Chromosome Location	chr18:13365259-13365260
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10084046	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1107340	0.88[CEU][hapmap];0.91[JPT][hapmap]
rs1107341	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11080642	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12959091	0.84[CHB][hapmap]
rs16940349	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs17681406	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2085050	0.82[CHB][hapmap]
rs2187502	0.82[CHB][hapmap];0.87[CHD][hapmap];0.82[MEX][hapmap]
rs2276392	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs2867874	0.86[CHB][hapmap]
rs35815061	0.80[ASN][1000 genomes]
rs4570934	0.82[CHB][hapmap]
rs4570935	0.86[CHB][hapmap]
rs4602105	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4797764	0.91[JPT][hapmap]
rs6505798	0.86[MEX][hapmap]
rs6505802	0.81[AMR][1000 genomes]
rs6505807	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6505808	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7226901	0.82[CHB][hapmap]
rs7227361	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7229983	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7231366	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7234501	0.82[CHB][hapmap]
rs7236152	0.80[CHB][hapmap]
rs7236934	0.80[AMR][1000 genomes]
rs7237577	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7241410	0.86[CHB][hapmap]
rs7241438	0.84[CHD][hapmap]
rs7242024	0.86[CHB][hapmap];0.81[AMR][1000 genomes]
rs7242140	0.91[CHB][hapmap];0.81[AMR][1000 genomes]
rs8087505	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[MEX][hapmap]
rs8088874	0.90[ASN][1000 genomes]
rs8094197	0.87[CHB][hapmap]
rs930797	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs930798	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[MEX][hapmap]
rs930799	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs949259	0.91[CHB][hapmap]
rs981621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9946524	0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9947830	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9948620	0.96[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9952682	0.81[AMR][1000 genomes]
rs9952836	0.82[GIH][hapmap];0.82[MEX][hapmap]
rs9953274	0.82[CHB][hapmap];0.87[CHD][hapmap];0.81[MEX][hapmap]
rs9954359	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs9954816	0.97[ASN][1000 genomes]
rs9957334	0.94[ASN][1000 genomes]
rs9960893	0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
rs11080646	TUBB6	cis	cerebellum	SCAN
rs11080646	AFG3L2	cis	cerebellum	SCAN
rs11080646	C18orf19	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13351800-13374800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr18:13354200-13371800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr18:13354200-13372000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr18:13354400-13371200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr18:13355000-13374200	Weak transcription	Dnd41	blood
6	chr18:13356400-13379200	Weak transcription	Aorta	Aorta
7	chr18:13359400-13379400	Weak transcription	Psoas Muscle	Psoas
8	chr18:13360000-13366600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr18:13360200-13366800	Weak transcription	Brain Substantia Nigra	brain
10	chr18:13361600-13365800	Enhancers	Fetal Brain Male	brain
11	chr18:13361600-13369400	Weak transcription	Pancreas	Pancrea
12	chr18:13362000-13367200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr18:13362000-13374600	Weak transcription	Fetal Muscle Leg	muscle
14	chr18:13363200-13367200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr18:13363200-13369800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr18:13363600-13366600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr18:13363600-13366800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr18:13363600-13369200	Weak transcription	Fetal Heart	heart
19	chr18:13363800-13366800	Weak transcription	Brain Germinal Matrix	brain
20	chr18:13364200-13371400	Enhancers	Fetal Thymus	thymus
21	chr18:13364400-13365600	Strong transcription	Thymus	Thymus
22	chr18:13364400-13365800	Enhancers	Liver	Liver
23	chr18:13364600-13365400	Enhancers	Right Ventricle	heart
24	chr18:13364600-13365600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr18:13364600-13365600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr18:13364600-13365800	Enhancers	Colon Smooth Muscle	Colon
27	chr18:13364600-13365800	Enhancers	Fetal Stomach	stomach
28	chr18:13364800-13365400	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr18:13364800-13365400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr18:13364800-13365400	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr18:13364800-13365600	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr18:13364800-13365600	Enhancers	Brain Hippocampus Middle	brain
33	chr18:13364800-13365600	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr18:13364800-13365600	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr18:13364800-13365600	Enhancers	Rectal Smooth Muscle	rectum
36	chr18:13364800-13365800	Enhancers	H1 Cell Line	embryonic stem cell
37	chr18:13364800-13365800	Enhancers	Fetal Brain Female	brain
38	chr18:13365000-13365400	Enhancers	H9 Cell Line	embryonic stem cell
39	chr18:13365000-13365400	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr18:13365000-13369000	Weak transcription	HepG2	liver
41	chr18:13365200-13365400	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr18:13365200-13366200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr18:13365200-13367000	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr18:13365200-13367000	Weak transcription	Left Ventricle	heart
45	chr18:13365200-13367400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr18:13365200-13367400	Weak transcription	Right Atrium	heart
47	chr18:13365200-13367600	Weak transcription	Spleen	Spleen
48	chr18:13365200-13368800	Enhancers	Brain Anterior Caudate	brain
49	chr18:13365200-13369400	Weak transcription	Primary T cells from cord blood	blood
50	chr18:13365200-13372200	Weak transcription	Brain Angular Gyrus	brain

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