Variant report

Variant	rs2279075
Chromosome Location	chr18:8343765-8343766
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:8336321..8338584-chr18:8341680..8343766,3	K562	blood:

Variant related genes	Relation type
ENSG00000268046	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11873504	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11873699	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs11875935	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11876724	0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11876786	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11877672	0.83[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12456630	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12954518	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12966511	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1542451	0.84[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17490458	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]
rs17490807	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs17490828	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]
rs2246146	0.88[CEU][hapmap]
rs2279074	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35431779	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36032451	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56137612	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs594691	1.00[YRI][hapmap]
rs595649	1.00[YRI][hapmap]
rs603504	0.89[JPT][hapmap]
rs62085046	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs685144	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7226445	0.81[ASW][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7244164	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[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]
rs754140	0.80[CEU][hapmap]
rs8087223	1.00[ASW][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][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
rs2279075	TUBB6	cis	cerebellum	SCAN

Chromatin state (count:48 , 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	chr18:8339400-8344200	Enhancers	Fetal Heart	heart
5	chr18:8339600-8344000	Enhancers	Fetal Lung	lung
6	chr18:8340200-8344200	Weak transcription	Brain Anterior Caudate	brain
7	chr18:8340200-8365600	Weak transcription	Psoas Muscle	Psoas
8	chr18:8340800-8344200	Enhancers	Stomach Mucosa	stomach
9	chr18:8341200-8343800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr18:8341600-8348800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr18:8342000-8346000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr18:8342000-8346000	Weak transcription	Ovary	ovary
13	chr18:8342000-8346200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr18:8342000-8346200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr18:8342000-8348200	Weak transcription	Fetal Intestine Large	intestine
16	chr18:8342000-8359200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr18:8342000-8362400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr18:8342200-8343800	Enhancers	HepG2	liver
19	chr18:8342200-8346000	Weak transcription	Fetal Stomach	stomach
20	chr18:8342200-8346000	Weak transcription	Lung	lung
21	chr18:8342200-8346200	Weak transcription	Fetal Intestine Small	intestine
22	chr18:8342200-8348200	Weak transcription	Pancreas	Pancrea
23	chr18:8342200-8349000	Weak transcription	Hela-S3	cervix
24	chr18:8342200-8350200	Weak transcription	Fetal Muscle Leg	muscle
25	chr18:8342200-8354600	Weak transcription	Gastric	stomach
26	chr18:8342200-8354600	Weak transcription	Left Ventricle	heart
27	chr18:8342200-8355200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr18:8342200-8359600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr18:8342200-8366800	Weak transcription	Adipose Nuclei	Adipose
30	chr18:8342200-8367400	Weak transcription	Aorta	Aorta
31	chr18:8342400-8344800	Weak transcription	NHLF	lung
32	chr18:8342400-8346600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr18:8342400-8346600	Weak transcription	NHDF-Ad	bronchial
34	chr18:8342400-8347000	Weak transcription	Brain Hippocampus Middle	brain
35	chr18:8342600-8345800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr18:8342600-8348000	Weak transcription	Osteobl	bone
37	chr18:8342600-8349400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr18:8342600-8349600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr18:8342600-8350400	Weak transcription	HSMMtube	muscle
40	chr18:8342600-8366400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr18:8342800-8357600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr18:8343000-8351800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr18:8343200-8344000	Enhancers	Fetal Kidney	kidney
44	chr18:8343400-8344000	Enhancers	Right Atrium	heart
45	chr18:8343400-8344000	Enhancers	Right Ventricle	heart
46	chr18:8343600-8344200	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr18:8343600-8344200	Genic enhancers	A549	lung
48	chr18:8343600-8346000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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