Variant report

Variant	rs9948620
Chromosome Location	chr18:13358206-13358207
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10084046	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs1107340	0.84[CEU][hapmap]
rs1107341	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11080646	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]
rs12456859	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12604142	0.84[JPT][hapmap]
rs12961452	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1454128	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16940349	0.86[MEX][hapmap]
rs17681406	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1869497	0.81[JPT][hapmap]
rs2187502	0.82[MEX][hapmap]
rs4602105	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6505807	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6505808	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7229983	0.90[EUR][1000 genomes]
rs7231366	0.96[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs7234675	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7237577	0.96[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7241438	0.86[MEX][hapmap]
rs8087505	0.82[MEX][hapmap]
rs8092304	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs897035	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs897036	0.90[JPT][hapmap]
rs930797	0.82[MEX][hapmap]
rs930798	0.82[MEX][hapmap]
rs981621	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9947830	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9952836	0.92[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9953274	0.81[MEX][hapmap]
rs9957335	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9957621	0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.92[ASN][1000 genomes]
rs9963572	0.85[JPT][hapmap]

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
rs9948620	TUBB6	cis	cerebellum	SCAN
rs9948620	C18orf19	cis	cerebellum	SCAN
rs9948620	AFG3L2	cis	cerebellum	SCAN

Chromatin state (count:22 , 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	chr18:13353800-13359000	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr18:13353800-13359000	Weak transcription	Primary B cells from cord blood	blood
4	chr18:13353800-13359000	Weak transcription	Psoas Muscle	Psoas
5	chr18:13353800-13359200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr18:13353800-13359200	Weak transcription	Brain Anterior Caudate	brain
7	chr18:13353800-13361000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr18:13353800-13361600	Weak transcription	Right Atrium	heart
9	chr18:13354200-13371800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr18:13354200-13372000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr18:13354400-13359200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr18:13354400-13371200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr18:13355000-13359000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr18:13355000-13374200	Weak transcription	Dnd41	blood
15	chr18:13355200-13359000	Weak transcription	Left Ventricle	heart
16	chr18:13356200-13360800	Weak transcription	Right Ventricle	heart
17	chr18:13356400-13359000	Weak transcription	Fetal Thymus	thymus
18	chr18:13356400-13359000	Weak transcription	Thymus	Thymus
19	chr18:13356400-13379200	Weak transcription	Aorta	Aorta
20	chr18:13357000-13358400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr18:13357800-13359000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr18:13358000-13359000	Weak transcription	Monocytes-CD14+_RO01746	blood

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