Variant report

Variant	rs11662978
Chromosome Location	chr18:12287976-12287977
allele	A/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	ZNF263	chr18:12287266-12288260	HEK293-T-REx	kidney:	n/a	chr18:12287668-12287677
2	MAX	chr18:12287569-12288553	ECC-1	luminal epithelium:	n/a	chr18:12287803-12287813 chr18:12287856-12287866
3	SIN3AK20	chr18:12287971-12288392	SK-N-SH	brain:	n/a	n/a
4	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
5	MXI1	chr18:12287944-12288369	Hela-S3	cervix:	n/a	n/a
6	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
7	MAZ	chr18:12287875-12288461	K562	blood:	n/a	n/a
8	TCF12	chr18:12287726-12289097	ECC-1	luminal epithelium:	n/a	chr18:12288199-12288206 chr18:12288197-12288207 chr18:12288632-12288639
9	POLR2A	chr18:12287777-12288457	Gliobla	brain:	n/a	n/a
10	ZBTB7A	chr18:12287414-12288704	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr18:12287798-12288555	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr18:12287521-12288343	MCF10A-Er-Src	breast:	n/a	n/a
13	USF1	chr18:12287869-12288500	ECC-1	luminal epithelium:	n/a	n/a
14	ZKSCAN1	chr18:12287914-12288277	Hela-S3	cervix:	n/a	n/a
15	MAX	chr18:12287327-12288525	ECC-1	luminal epithelium:	n/a	chr18:12287803-12287813 chr18:12287856-12287866
16	POLR2A	chr18:12287819-12288459	ECC-1	luminal epithelium:	n/a	n/a
17	TAF1	chr18:12287734-12288455	ECC-1	luminal epithelium:	n/a	n/a
18	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
19	E2F6	chr18:12287937-12288092	K562	blood:	n/a	n/a
20	TEAD4	chr18:12287354-12288633	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr18:12286987-12289319	IMR90	lung:	n/a	n/a
22	CTCF	chr18:12287860-12288010	Caco-2	colon:	n/a	n/a
23	UBTF	chr18:12287812-12288619	K562	blood:	n/a	n/a
24	GTF2F1	chr18:12287968-12288448	Hela-S3	cervix:	n/a	n/a
25	SIN3A	chr18:12287134-12289055	H1-hESC	embryonic stem cell:	n/a	chr18:12287919-12287930 chr18:12287299-12287310
26	MAZ	chr18:12287775-12288422	Hela-S3	cervix:	n/a	chr18:12287803-12287813 chr18:12287856-12287866
27	CTCF	chr18:12287840-12287990	GM12871	blood:	n/a	chr18:12287855-12287868 chr18:12287853-12287866
28	CTCF	chr18:12287768-12288040	IMR90	lung:	n/a	chr18:12287855-12287868 chr18:12287853-12287866
29	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
30	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
31	MAX	chr18:12287754-12287984	K562	blood:	n/a	chr18:12287803-12287813 chr18:12287856-12287866
32	MAX	chr18:12287069-12288484	H1-hESC	embryonic stem cell:	n/a	chr18:12287803-12287813 chr18:12287856-12287866
33	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
34	TCF12	chr18:12287472-12288560	ECC-1	luminal epithelium:	n/a	chr18:12288199-12288206 chr18:12288197-12288207
35	BHLHE40	chr18:12287822-12288595	K562	blood:	n/a	chr18:12287853-12287869 chr18:12287850-12287866
36	POLR2A	chr18:12287803-12288418	ProgFib	skin:	n/a	n/a
37	CTCF	chr18:12287840-12287990	HMF	breast:	n/a	chr18:12287855-12287868 chr18:12287853-12287866
38	POLR2A	chr18:12287918-12288397	HCT-116	colon:	n/a	n/a
39	POLR2A	chr18:12287648-12288679	U87	brain:	n/a	n/a
40	POLR2A	chr18:12287923-12288298	HCT-116	colon:	n/a	n/a
41	POLR2A	chr18:12287856-12288513	Hela-S3	cervix:	n/a	n/a
42	MAFK	chr18:12287954-12288433	IMR90	lung:	n/a	n/a
43	SMC3	chr18:12287707-12288385	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr18:12287886-12288447	Hela-S3	cervix:	n/a	n/a
45	CCNT2	chr18:12287927-12288392	K562	blood:	n/a	n/a
46	POLR2A	chr18:12287965-12288646	K562	blood:	n/a	n/a
47	CTBP2	chr18:12287123-12289209	H1-hESC	embryonic stem cell:	n/a	n/a
48	MYC	chr18:12287625-12288325	MCF10A-Er-Src	breast:	n/a	chr18:12287803-12287813 chr18:12287856-12287866
49	RCOR1	chr18:12287787-12288374	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr18:12287765-12288573	U87	brain:	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: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs4797667	0.84[AFR][1000 genomes]
rs4797668	0.84[AFR][1000 genomes]
rs4797669	0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6505747	1.00[YRI][hapmap]
rs7505097	0.84[AFR][1000 genomes]
rs7505123	1.00[YRI][hapmap]
rs7505582	0.88[AFR][1000 genomes]
rs7506533	0.85[AFR][1000 genomes]
rs7506586	1.00[YRI][hapmap]
rs8084284	0.84[AFR][1000 genomes]
rs9953917	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9956239	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9960329	1.00[YRI][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

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12287000-12288000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr18:12287000-12288400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr18:12287000-12289000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr18:12287200-12288000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr18:12287200-12288000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr18:12287200-12288000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr18:12287200-12288000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
8	chr18:12287200-12288000	Flanking Active TSS	HMEC	breast
9	chr18:12287200-12288000	Flanking Active TSS	HSMMtube	muscle
10	chr18:12287200-12288200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr18:12287200-12288400	Active TSS	Colon Smooth Muscle	Colon
12	chr18:12287200-12288400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
13	chr18:12287200-12288600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr18:12287200-12288600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr18:12287200-12289000	Bivalent Enhancer	Fetal Brain Male	brain
16	chr18:12287200-12289200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr18:12287200-12289400	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr18:12287400-12288000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr18:12287400-12288000	Bivalent Enhancer	Liver	Liver
20	chr18:12287400-12288000	Flanking Active TSS	Pancreas	Pancrea
21	chr18:12287400-12288000	Flanking Active TSS	HSMM	muscle
22	chr18:12287400-12288000	Flanking Active TSS	NHLF	lung
23	chr18:12287400-12288400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr18:12287400-12288400	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr18:12287400-12288400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr18:12287400-12288600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr18:12287400-12288600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr18:12287400-12288600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr18:12287400-12288600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
30	chr18:12287400-12288600	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
31	chr18:12287400-12288600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
32	chr18:12287400-12288800	Active TSS	H9 Cell Line	embryonic stem cell
33	chr18:12287400-12288800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
34	chr18:12287400-12288800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
35	chr18:12287400-12289000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
36	chr18:12287400-12289000	Active TSS	Esophagus	oesophagus
37	chr18:12287400-12289400	Flanking Active TSS	NHEK	skin
38	chr18:12287600-12288000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
39	chr18:12287600-12288000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr18:12287600-12288000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
41	chr18:12287600-12288000	Bivalent Enhancer	Fetal Lung	lung
42	chr18:12287600-12288000	Active TSS	Placenta Amnion	Placenta Amnion
43	chr18:12287600-12288000	Active TSS	Right Ventricle	heart
44	chr18:12287600-12288000	Flanking Active TSS	Hela-S3	cervix
45	chr18:12287600-12288000	Bivalent/Poised TSS	HepG2	liver
46	chr18:12287600-12288200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr18:12287600-12288200	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr18:12287600-12288200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr18:12287600-12288200	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
50	chr18:12287600-12288200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum

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