Variant report

Variant	rs8093494
Chromosome Location	chr18:12288111-12288112
allele	C/T
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	MYC	chr18:12288043-12288395	K562	blood:	n/a	n/a
2	MYC	chr18:12288079-12288528	K562	blood:	n/a	n/a
3	ZNF263	chr18:12287266-12288260	HEK293-T-REx	kidney:	n/a	chr18:12287668-12287677
4	ZMIZ1	chr18:12288098-12288436	K562	blood:	n/a	n/a
5	FOS	chr18:12288092-12288328	MCF10A-Er-Src	breast:	n/a	n/a
6	TAL1	chr18:12288086-12288375	K562	blood:	n/a	n/a
7	MAX	chr18:12287569-12288553	ECC-1	luminal epithelium:	n/a	chr18:12287803-12287813 chr18:12287856-12287866
8	USF1	chr18:12288072-12288304	H1-hESC	embryonic stem cell:	n/a	n/a
9	SIN3AK20	chr18:12287971-12288392	SK-N-SH	brain:	n/a	n/a
10	EGR1	chr18:12287812-12288334	ECC-1	luminal epithelium:	n/a	chr18:12288090-12288103 chr18:12288086-12288108 chr18:12288093-12288102 chr18:12287855-12287865 chr18:12288091-12288102 chr18:12288090-12288103 chr18:12288092-12288101 chr18:12288090-12288103 chr18:12288091-12288102 chr18:12288092-12288102 chr18:12287856-12287869 chr18:12288090-12288104 chr18:12288089-12288104 chr18:12288092-12288102
11	MXI1	chr18:12287944-12288369	Hela-S3	cervix:	n/a	n/a
12	MYC	chr18:12287984-12288284	MCF10A-Er-Src	breast:	n/a	n/a
13	EGR1	chr18:12287859-12288363	MCF-7	breast:	n/a	chr18:12288090-12288103 chr18:12288086-12288108 chr18:12288093-12288102 chr18:12288091-12288102 chr18:12288090-12288103 chr18:12288092-12288101 chr18:12288090-12288103 chr18:12288091-12288102 chr18:12288092-12288102 chr18:12288090-12288104 chr18:12288089-12288104 chr18:12288092-12288102
14	RFX5	chr18:12288022-12288505	Hela-S3	cervix:	n/a	n/a
15	BACH1	chr18:12287996-12288224	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr18:12288023-12288165	A549	lung:	n/a	n/a
17	MAZ	chr18:12287875-12288461	K562	blood:	n/a	n/a
18	TCF12	chr18:12287726-12289097	ECC-1	luminal epithelium:	n/a	chr18:12288199-12288206 chr18:12288197-12288207 chr18:12288632-12288639
19	POLR2A	chr18:12287777-12288457	Gliobla	brain:	n/a	n/a
20	ZBTB7A	chr18:12287414-12288704	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr18:12287798-12288555	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr18:12287521-12288343	MCF10A-Er-Src	breast:	n/a	n/a
23	USF1	chr18:12287869-12288500	ECC-1	luminal epithelium:	n/a	n/a
24	USF1	chr18:12288036-12288400	SK-N-SH	brain:	n/a	n/a
25	TBP	chr18:12288071-12288367	Hela-S3	cervix:	n/a	n/a
26	ZKSCAN1	chr18:12287914-12288277	Hela-S3	cervix:	n/a	n/a
27	MAX	chr18:12287327-12288525	ECC-1	luminal epithelium:	n/a	chr18:12287803-12287813 chr18:12287856-12287866
28	POLR2A	chr18:12287819-12288459	ECC-1	luminal epithelium:	n/a	n/a
29	TAF1	chr18:12287734-12288455	ECC-1	luminal epithelium:	n/a	n/a
30	EGR1	chr18:12287546-12288541	HCT-116	colon:	n/a	chr18:12288090-12288103 chr18:12288086-12288108 chr18:12288093-12288102 chr18:12287855-12287865 chr18:12288091-12288102 chr18:12288090-12288103 chr18:12287617-12287626 chr18:12288092-12288101 chr18:12288090-12288103 chr18:12288091-12288102 chr18:12288092-12288102 chr18:12287856-12287869 chr18:12288090-12288104 chr18:12288089-12288104 chr18:12288092-12288102
31	TEAD4	chr18:12287354-12288633	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr18:12286987-12289319	IMR90	lung:	n/a	n/a
33	UBTF	chr18:12287812-12288619	K562	blood:	n/a	n/a
34	GTF2F1	chr18:12287968-12288448	Hela-S3	cervix:	n/a	n/a
35	SIN3A	chr18:12287134-12289055	H1-hESC	embryonic stem cell:	n/a	chr18:12287919-12287930 chr18:12287299-12287310
36	MAZ	chr18:12287775-12288422	Hela-S3	cervix:	n/a	chr18:12287803-12287813 chr18:12287856-12287866
37	CTCF	chr18:12288020-12288170	AG04449	skin:	n/a	n/a
38	TEAD4	chr18:12287997-12288435	K562	blood:	n/a	n/a
39	FOS	chr18:12288088-12288278	MCF10A-Er-Src	breast:	n/a	n/a
40	EGR1	chr18:12287561-12288546	HCT-116	colon:	n/a	chr18:12288090-12288103 chr18:12288086-12288108 chr18:12288093-12288102 chr18:12287855-12287865 chr18:12288091-12288102 chr18:12288090-12288103 chr18:12287617-12287626 chr18:12288092-12288101 chr18:12288090-12288103 chr18:12288091-12288102 chr18:12288092-12288102 chr18:12287856-12287869 chr18:12288090-12288104 chr18:12288089-12288104 chr18:12288092-12288102
41	EGR1	chr18:12287750-12288272	K562	blood:	n/a	chr18:12288090-12288103 chr18:12288086-12288108 chr18:12288093-12288102 chr18:12287855-12287865 chr18:12288091-12288102 chr18:12288090-12288103 chr18:12288092-12288101 chr18:12288090-12288103 chr18:12288091-12288102 chr18:12288092-12288102 chr18:12287856-12287869 chr18:12288090-12288104 chr18:12288089-12288104 chr18:12288092-12288102
42	RCOR1	chr18:12288108-12288252	HepG2	liver:	n/a	n/a
43	MAX	chr18:12287069-12288484	H1-hESC	embryonic stem cell:	n/a	chr18:12287803-12287813 chr18:12287856-12287866
44	EGR1	chr18:12287869-12288317	H1-hESC	embryonic stem cell:	n/a	chr18:12288090-12288103 chr18:12288086-12288108 chr18:12288093-12288102 chr18:12288091-12288102 chr18:12288090-12288103 chr18:12288092-12288101 chr18:12288090-12288103 chr18:12288091-12288102 chr18:12288092-12288102 chr18:12288090-12288104 chr18:12288089-12288104 chr18:12288092-12288102
45	USF2	chr18:12288104-12288252	H1-hESC	embryonic stem cell:	n/a	n/a
46	TCF12	chr18:12287472-12288560	ECC-1	luminal epithelium:	n/a	chr18:12288199-12288206 chr18:12288197-12288207
47	BHLHE40	chr18:12287822-12288595	K562	blood:	n/a	chr18:12287853-12287869 chr18:12287850-12287866
48	JUND	chr18:12288082-12288387	K562	blood:	n/a	n/a
49	POLR2A	chr18:12287803-12288418	ProgFib	skin:	n/a	n/a
50	POLR2A	chr18:12287918-12288397	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12282475..12288140-chr18:12305542..12311210,9	K562	blood:

Variant related genes	Relation type
ENSG00000267069	TF binding region
ENSG00000176014	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12966726	0.89[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs35526008	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6505744	0.83[GIH][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv909401	chr18:12211483-12312075	Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv909402	chr18:12211483-12325222	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv909403	chr18:12231060-12325222	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1061545	chr18:12235999-12328405	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv870342	chr18:12270808-12295798	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1058661	chr18:12280366-12313865	Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8093494	TUBB6	cis	multi-tissue	Pritchard
rs8093494	TUBB6	cis	lymphoblastoid	seeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12287000-12288400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr18:12287000-12289000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr18:12287200-12288200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr18:12287200-12288400	Active TSS	Colon Smooth Muscle	Colon
5	chr18:12287200-12288400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
6	chr18:12287200-12288600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr18:12287200-12288600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
8	chr18:12287200-12289000	Bivalent Enhancer	Fetal Brain Male	brain
9	chr18:12287200-12289200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr18:12287200-12289400	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr18:12287400-12288400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr18:12287400-12288400	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr18:12287400-12288400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr18:12287400-12288600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr18:12287400-12288600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr18:12287400-12288600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr18:12287400-12288600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
18	chr18:12287400-12288600	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
19	chr18:12287400-12288600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
20	chr18:12287400-12288800	Active TSS	H9 Cell Line	embryonic stem cell
21	chr18:12287400-12288800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
22	chr18:12287400-12288800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
23	chr18:12287400-12289000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
24	chr18:12287400-12289000	Active TSS	Esophagus	oesophagus
25	chr18:12287400-12289400	Flanking Active TSS	NHEK	skin
26	chr18:12287600-12288200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr18:12287600-12288200	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr18:12287600-12288200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr18:12287600-12288200	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
30	chr18:12287600-12288200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
31	chr18:12287600-12288200	Active TSS	Osteobl	bone
32	chr18:12287600-12288400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr18:12287600-12288400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr18:12287600-12288400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr18:12287600-12288400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr18:12287600-12288400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr18:12287600-12288400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
38	chr18:12287600-12288400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
39	chr18:12287600-12288400	Active TSS	A549	lung
40	chr18:12287600-12288400	Flanking Active TSS	HUVEC	blood vessel
41	chr18:12287600-12288600	Active TSS	Aorta	Aorta
42	chr18:12287600-12288600	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
43	chr18:12287600-12288600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
44	chr18:12287600-12288600	Flanking Active TSS	Brain Substantia Nigra	brain
45	chr18:12287600-12288600	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
46	chr18:12287600-12288600	Flanking Bivalent TSS/Enh	Placenta	Placenta
47	chr18:12287600-12288600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
48	chr18:12287600-12288800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr18:12287600-12288800	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
50	chr18:12287600-12289000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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