Variant report

Variant	rs17490828
Chromosome Location	chr18:8351449-8351450
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11873504	0.90[CHB][hapmap];0.81[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11873699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11876724	0.86[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11876786	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11877672	0.92[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12456630	0.81[CHB][hapmap];0.86[CHD][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs12954518	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12966511	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1459173	0.85[YRI][hapmap]
rs1542451	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17490458	0.81[CHB][hapmap];0.95[CHD][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17490807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017965	0.87[YRI][hapmap]
rs2017988	0.87[YRI][hapmap]
rs2242148	0.87[YRI][hapmap]
rs2279074	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279075	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35431779	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36032451	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56137612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594691	0.88[YRI][hapmap]
rs595649	0.88[YRI][hapmap]
rs603504	0.89[JPT][hapmap]
rs62085046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs685144	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs7226445	0.81[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7244164	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8087223	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][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	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv458018	chr18:8110805-8645907	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv576426	chr18:8110805-8645907	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	esv3351324	chr18:8250514-8405140	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1058445	chr18:8270681-8421249	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17490828	TUBB6	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:8320800-8357200	Weak transcription	Thymus	Thymus
2	chr18:8329600-8358200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr18:8329800-8365200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr18:8340200-8365600	Weak transcription	Psoas Muscle	Psoas
5	chr18:8342000-8359200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr18:8342000-8362400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr18:8342200-8354600	Weak transcription	Gastric	stomach
8	chr18:8342200-8354600	Weak transcription	Left Ventricle	heart
9	chr18:8342200-8355200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:8342200-8359600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr18:8342200-8366800	Weak transcription	Adipose Nuclei	Adipose
12	chr18:8342200-8367400	Weak transcription	Aorta	Aorta
13	chr18:8342600-8366400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr18:8342800-8357600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr18:8343000-8351800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr18:8344000-8353800	Weak transcription	Right Ventricle	heart
17	chr18:8344200-8356600	Weak transcription	A549	lung
18	chr18:8344200-8367000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr18:8345400-8358200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr18:8346400-8366800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr18:8346600-8358200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr18:8346600-8358800	Weak transcription	Ovary	ovary
23	chr18:8348400-8351800	Weak transcription	Fetal Stomach	stomach
24	chr18:8348600-8359200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr18:8349600-8351600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr18:8350200-8362000	Weak transcription	Lung	lung
27	chr18:8350200-8366200	Weak transcription	Pancreas	Pancrea
28	chr18:8350200-8367200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr18:8350400-8351600	Enhancers	HSMMtube	muscle
30	chr18:8350400-8359800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr18:8350600-8354400	Weak transcription	HepG2	liver
32	chr18:8350800-8352400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr18:8351000-8352000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr18:8351000-8354200	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links