Variant report

Variant	rs17490458
Chromosome Location	chr18:8341170-8341171
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr18:8341159-8342758	A549	lung:	n/a	n/a
2	EP300	chr18:8341160-8342748	A549	lung:	n/a	chr18:8342167-8342180 chr18:8342057-8342071
3	SP1	chr18:8341083-8342685	A549	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000268046	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11873504	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11873699	0.81[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11875935	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11876724	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11876786	0.92[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11877672	1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs12456630	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12954518	0.81[EUR][1000 genomes]
rs12966511	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1459173	0.85[YRI][hapmap]
rs1542451	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17490807	0.81[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17490828	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]
rs2017965	0.87[YRI][hapmap]
rs2017988	0.87[YRI][hapmap]
rs2242148	0.87[YRI][hapmap]
rs2246146	0.81[CEU][hapmap]
rs2279074	0.92[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2279075	0.92[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35431779	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36032451	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56137612	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs594691	0.84[JPT][hapmap];0.88[YRI][hapmap]
rs595649	0.84[JPT][hapmap];0.88[YRI][hapmap]
rs62085046	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs685144	0.94[CEU][hapmap]
rs7226445	0.91[CHD][hapmap];0.84[AMR][1000 genomes]
rs7244164	0.81[CHB][hapmap];0.95[CHD][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs754140	0.88[CEU][hapmap]
rs8087223	0.95[CHD][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1057288	chr18:8218725-8351340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv543639	chr18:8218725-8351340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	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
7	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
rs17490458	TUBB6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:8294200-8341400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr18:8319800-8341600	Weak transcription	Adipose Nuclei	Adipose
3	chr18:8320800-8357200	Weak transcription	Thymus	Thymus
4	chr18:8321200-8341400	Weak transcription	Lung	lung
5	chr18:8325800-8341200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr18:8328000-8342600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr18:8329000-8341400	Weak transcription	Fetal Stomach	stomach
8	chr18:8329000-8341400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr18:8329600-8358200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr18:8329800-8365200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr18:8330400-8341600	Weak transcription	Fetal Muscle Leg	muscle
12	chr18:8330600-8341400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr18:8332000-8341400	Weak transcription	Fetal Intestine Small	intestine
14	chr18:8334400-8341800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr18:8334600-8341200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr18:8337000-8341400	Weak transcription	Small Intestine	intestine
17	chr18:8337800-8341600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr18:8338800-8341400	Enhancers	HepG2	liver
19	chr18:8339000-8341200	Enhancers	A549	lung
20	chr18:8339400-8342000	Enhancers	Right Atrium	heart
21	chr18:8339400-8342200	Enhancers	Left Ventricle	heart
22	chr18:8339400-8342200	Enhancers	Right Ventricle	heart
23	chr18:8339400-8342600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr18:8339400-8344200	Enhancers	Fetal Heart	heart
25	chr18:8339600-8342200	Enhancers	Pancreas	Pancrea
26	chr18:8339600-8344000	Enhancers	Fetal Lung	lung
27	chr18:8339800-8341400	Weak transcription	Ovary	ovary
28	chr18:8339800-8341400	Weak transcription	NHLF	lung
29	chr18:8340200-8341400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr18:8340200-8341400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr18:8340200-8341400	Weak transcription	Gastric	stomach
32	chr18:8340200-8344200	Weak transcription	Brain Anterior Caudate	brain
33	chr18:8340200-8365600	Weak transcription	Psoas Muscle	Psoas
34	chr18:8340400-8342200	Enhancers	Aorta	Aorta
35	chr18:8340600-8341200	Weak transcription	Osteobl	bone
36	chr18:8340800-8341800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr18:8340800-8343000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr18:8340800-8344200	Enhancers	Stomach Mucosa	stomach
39	chr18:8341000-8341200	Weak transcription	Brain Hippocampus Middle	brain
40	chr18:8341000-8342000	Enhancers	HSMMtube	muscle
41	chr18:8341000-8342200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr18:8341000-8343000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr18:8341000-8343000	Enhancers	Liver	Liver

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