Variant report

Variant	rs540538307
Chromosome Location	chr18:11980668-11980669
allele	A/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	SIN3AK20	chr18:11980129-11981539	MCF-7	breast:	n/a	n/a
2	CHD2	chr18:11980124-11981266	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAFK	chr18:11980333-11980777	K562	blood:	n/a	n/a
4	CTCF	chr18:11980518-11980687	GM12878	blood:	n/a	n/a
5	CTCF	chr18:11980520-11980670	GM12867	blood:	n/a	n/a
6	TAF1	chr18:11980502-11981065	A549	lung:	n/a	n/a
7	SIN3AK20	chr18:11980524-11980928	PANC-1	pancreas:	n/a	n/a
8	SP1	chr18:11980355-11981448	H1-hESC	embryonic stem cell:	n/a	chr18:11981114-11981124 chr18:11981000-11981012 chr18:11981115-11981124 chr18:11981187-11981201 chr18:11980964-11980973 chr18:11981001-11981010 chr18:11980934-11980943 chr18:11981002-11981011 chr18:11980933-11980942 chr18:11980932-11980943 chr18:11980964-11980973 chr18:11981115-11981124 chr18:11980963-11980972 chr18:11981192-11981201 chr18:11980997-11981011 chr18:11980932-11980944 chr18:11981113-11981125 chr18:11980933-11980943 chr18:11980851-11980862 chr18:11980963-11980973 chr18:11981192-11981201 chr18:11981114-11981123 chr18:11981190-11981202 chr18:11981113-11981125 chr18:11980932-11980944 chr18:11981191-11981200 chr18:11981190-11981202 chr18:11981191-11981201 chr18:11980962-11980974 chr18:11980962-11980974 chr18:11980933-11980943 chr18:11981191-11981201 chr18:11981000-11981012 chr18:11981114-11981124
9	CTCF	chr18:11980540-11980690	MCF-7	breast:	n/a	n/a
10	POLR2A	chr18:11980317-11981106	K562	blood:	n/a	n/a
11	TBL1XR1	chr18:11980179-11981225	K562	blood:	n/a	n/a
12	MYBL2	chr18:11980106-11981205	HepG2	liver:	n/a	n/a
13	POLR2A	chr18:11980348-11981830	GM19099	blood:	n/a	n/a
14	POLR2A	chr18:11980370-11981236	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr18:11980409-11980858	K562	blood:	n/a	n/a
16	POLR2A	chr18:11980046-11981745	MCF10A-Er-Src	breast:	n/a	n/a
17	TCF12	chr18:11980561-11981436	ECC-1	luminal epithelium:	n/a	chr18:11980676-11980686
18	UBTF	chr18:11980326-11982285	K562	blood:	n/a	n/a
19	CTCF	chr18:11980560-11980710	HRPEpiC	eye:	n/a	n/a
20	CEBPB	chr18:11980466-11980804	H1-hESC	embryonic stem cell:	n/a	n/a
21	TBP	chr18:11980367-11981096	HepG2	liver:	n/a	n/a
22	USF2	chr18:11980667-11980770	GM12878	blood:	n/a	n/a
23	CTCF	chr18:11980580-11980730	SAEC	small airway:	n/a	n/a
24	POLR2A	chr18:11980254-11981212	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr18:11979815-11984651	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr18:11980200-11982509	NB4	blood:	n/a	n/a
27	MYC	chr18:11980473-11981594	MCF-7	breast:	n/a	chr18:11980736-11980743 chr18:11980734-11980745 chr18:11980735-11980745 chr18:11980735-11980744 chr18:11980733-11980748
28	MAX	chr18:11980246-11981677	MCF-7	breast:	n/a	chr18:11980736-11980743 chr18:11980734-11980745 chr18:11980735-11980745 chr18:11980735-11980744 chr18:11980733-11980748
29	POLR2A	chr18:11979871-11982537	H1-hESC	embryonic stem cell:	n/a	n/a
30	RCOR1	chr18:11980391-11982280	HepG2	liver:	n/a	n/a
31	POLR2A	chr18:11980422-11981063	GM12892	blood:	n/a	n/a
32	POLR2A	chr18:11980483-11981131	PANC-1	pancreas:	n/a	n/a
33	CTCF	chr18:11980580-11980730	GM12866	blood:	n/a	n/a
34	MYC	chr18:11980220-11981254	K562	blood:	n/a	chr18:11980736-11980743 chr18:11980734-11980745 chr18:11980735-11980745 chr18:11980735-11980744 chr18:11980733-11980748
35	E2F6	chr18:11979875-11982298	K562	blood:	n/a	chr18:11980676-11980686 chr18:11981195-11981205 chr18:11981509-11981521 chr18:11981001-11981010
36	CTCF	chr18:11980520-11980670	HEK293	kidney:	n/a	n/a
37	MAX	chr18:11980060-11982421	A549	lung:	n/a	chr18:11980736-11980743 chr18:11981882-11981892 chr18:11980734-11980745 chr18:11980735-11980745 chr18:11980735-11980744 chr18:11981808-11981817 chr18:11980733-11980748
38	TAF1	chr18:11980356-11981214	H1-hESC	embryonic stem cell:	n/a	n/a
39	EP300	chr18:11980561-11981835	ECC-1	luminal epithelium:	n/a	chr18:11981485-11981501 chr18:11981211-11981227 chr18:11981626-11981642 chr18:11981201-11981217 chr18:11981487-11981503
40	MYC	chr18:11980211-11981212	H1-hESC	embryonic stem cell:	n/a	chr18:11980736-11980743 chr18:11980734-11980745 chr18:11980735-11980745 chr18:11980735-11980744 chr18:11980733-11980748
41	MYC	chr18:11980412-11981239	MCF-7	breast:	n/a	chr18:11980736-11980743 chr18:11980734-11980745 chr18:11980735-11980745 chr18:11980735-11980744 chr18:11980733-11980748
42	CHD2	chr18:11980387-11981172	K562	blood:	n/a	n/a
43	IRF1	chr18:11980104-11981222	K562	blood:	n/a	chr18:11980932-11980946 chr18:11981000-11981014 chr18:11981113-11981127 chr18:11980962-11980976 chr18:11981190-11981204
44	HA-E2F1	chr18:11980263-11981255	MCF-7	breast:	n/a	chr18:11980676-11980686 chr18:11981195-11981205 chr18:11981001-11981010
45	CTCF	chr18:11980520-11980670	SK-N-SH_RA	brain:	n/a	n/a
46	SIN3AK20	chr18:11980479-11980927	K562	blood:	n/a	n/a
47	MTA3	chr18:11980237-11980952	GM12878	blood:	n/a	n/a
48	BRCA1	chr18:11980153-11981274	Hela-S3	cervix:	n/a	n/a
49	E2F6	chr18:11980084-11981760	H1-hESC	embryonic stem cell:	n/a	chr18:11980676-11980686 chr18:11981195-11981205 chr18:11981509-11981521 chr18:11981001-11981010
50	POLR2A	chr18:11980052-11981172	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:28832088..28833058-chr18:11980322..11980977,2	Hela-S3	cervix:
2	chr18:11979615..11982143-chr18:12376173..12378788,2	K562	blood:
3	chr14:24682206..24682834-chr18:11980405..11981236,2	Hela-S3	cervix:
4	chr18:11848937..11853647-chr18:11979272..11982109,5	K562	blood:
5	chr18:11980301..11981116-chr8:80942163..80942686,2	Hela-S3	cervix:
6	chr18:11906925..11910950-chr18:11978930..11983753,7	MCF-7	breast:
7	chr18:11905898..11908508-chr18:11980358..11982828,3	K562	blood:
8	chr18:11978568..11983192-chr18:11993805..11998306,5	MCF-7	breast:
9	chr1:104068529..104069287-chr18:11980099..11980792,2	Hela-S3	cervix:
10	chr1:24285780..24286361-chr18:11980215..11981116,2	Hela-S3	cervix:
11	chr18:11979089..11980849-chr18:12109709..12111299,2	K562	blood:
12	chr18:11908235..11908915-chr18:11980031..11980748,2	Hela-S3	cervix:
13	chr18:11906869..11908788-chr18:11979428..11982249,2	K562	blood:
14	chr18:11937666..11938178-chr18:11980436..11980995,2	MCF-7	breast:
15	chr18:11977841..11980802-chr18:11983345..11984923,2	MCF-7	breast:
16	chr18:11979171..11983679-chr18:11993501..11995734,4	MCF-7	breast:
17	chr18:11848574..11852252-chr18:11979272..11982648,7	K562	blood:
18	chr18:11907153..11910661-chr18:11980045..11982514,4	MCF-7	breast:

Variant related genes	Relation type
IMPA2	TF binding region
ENSG00000154889	Chromatin interaction
ENSG00000180198	Chromatin interaction
ENSG00000255112	Chromatin interaction
ENSG00000141385	Chromatin interaction
ENSG00000254692	Chromatin interaction
ENSG00000266955	Chromatin interaction
ENSG00000254505	Chromatin interaction
ENSG00000189266	Chromatin interaction
ENSG00000147586	Chromatin interaction
ENSG00000273141	Chromatin interaction
ENSG00000185946	Chromatin interaction
ENSG00000267165	Chromatin interaction
ENSG00000242125	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv2758470	chr18:11897023-12076102	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv2758713	chr18:11897023-12076102	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	nsv576495	chr18:11917410-11986557	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv909385	chr18:11938102-11986557	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
8	nsv909386	chr18:11938102-12095950	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	nsv909387	chr18:11953187-11986557	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
10	esv3424914	chr18:11980377-11982925	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11979000-11980800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr18:11980000-11980800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr18:11980000-11980800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr18:11980000-11980800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr18:11980000-11980800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr18:11980000-11980800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr18:11980000-11980800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr18:11980000-11980800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr18:11980000-11980800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr18:11980000-11980800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr18:11980000-11980800	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr18:11980000-11980800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
13	chr18:11980000-11980800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr18:11980000-11980800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr18:11980000-11980800	Flanking Active TSS	GM12878-XiMat	blood
16	chr18:11980000-11980800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr18:11980000-11980800	Flanking Active TSS	NHEK	skin
18	chr18:11980000-11981000	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr18:11980000-11981000	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr18:11980000-11981000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr18:11980000-11982600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr18:11980000-11983200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr18:11980000-11983200	Active TSS	Psoas Muscle	Psoas
24	chr18:11980200-11980800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr18:11980200-11980800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr18:11980200-11980800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr18:11980200-11980800	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr18:11980200-11980800	Flanking Active TSS	Placenta	Placenta
29	chr18:11980200-11980800	Flanking Active TSS	HMEC	breast
30	chr18:11980200-11980800	Flanking Active TSS	HUVEC	blood vessel
31	chr18:11980200-11980800	Flanking Active TSS	NHLF	lung
32	chr18:11980200-11981000	Bivalent/Poised TSS	Thymus	Thymus
33	chr18:11980200-11981800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr18:11980200-11981800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr18:11980200-11981800	Active TSS	Brain Cingulate Gyrus	brain
36	chr18:11980200-11981800	Active TSS	Brain Hippocampus Middle	brain
37	chr18:11980200-11981800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr18:11980200-11982000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr18:11980200-11982000	Active TSS	Brain Anterior Caudate	brain
40	chr18:11980200-11982000	Active TSS	Fetal Brain Female	brain
41	chr18:11980200-11982000	Active TSS	Fetal Muscle Trunk	muscle
42	chr18:11980200-11982200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr18:11980200-11982200	Active TSS	HSMMtube	muscle
44	chr18:11980200-11982400	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr18:11980200-11982400	Active TSS	Aorta	Aorta
46	chr18:11980200-11982400	Active TSS	Brain Substantia Nigra	brain
47	chr18:11980200-11982400	Active TSS	Ovary	ovary
48	chr18:11980200-11982600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr18:11980200-11982600	Active TSS	Colon Smooth Muscle	Colon
50	chr18:11980200-11982600	Active TSS	Right Ventricle	heart

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