Variant report

Variant	rs552511999
Chromosome Location	chr18:28681252-28681253
allele	A/C
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	POLR2A	chr18:28681220-28681680	A549	lung:	n/a	n/a
2	NFIC	chr18:28681175-28681818	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr18:28681242-28681636	HepG2	liver:	n/a	n/a
4	UBTF	chr18:28680916-28682589	K562	blood:	n/a	n/a
5	HNF4A	chr18:28681053-28681335	HepG2	liver:	n/a	chr18:28681210-28681225
6	E2F6	chr18:28681092-28681654	K562	blood:	n/a	n/a
7	NR2F2	chr18:28680753-28681384	K562	blood:	n/a	n/a
8	TAF1	chr18:28681080-28681475	K562	blood:	n/a	n/a
9	POLR2A	chr18:28679636-28682676	K562	blood:	n/a	n/a
10	SRF	chr18:28680507-28681300	HCT-116	colon:	n/a	chr18:28680943-28680960 chr18:28680941-28680956 chr18:28680944-28680955 chr18:28680943-28680954 chr18:28680944-28680958 chr18:28680942-28680955 chr18:28680944-28680953 chr18:28680940-28680954 chr18:28680940-28680958 chr18:28680938-28680956
11	CHD2	chr18:28680604-28682111	K562	blood:	n/a	n/a
12	MAX	chr18:28680849-28682731	K562	blood:	n/a	chr18:28682136-28682146
13	GTF2B	chr18:28680720-28681360	K562	blood:	n/a	n/a
14	ZNF143	chr18:28680797-28682028	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr18:28680664-28682702	K562	blood:	n/a	n/a
16	POLR2A	chr18:28681138-28682741	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr18:28680526-28682609	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr18:28681094-28682118	HL-60	blood:	n/a	n/a
19	SMARCB1	chr18:28680936-28682599	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr18:28680764-28682668	H1-hESC	embryonic stem cell:	n/a	n/a
21	TAF1	chr18:28680997-28682614	K562	blood:	n/a	n/a
22	STAT5A	chr18:28680949-28681499	K562	blood:	n/a	chr18:28681230-28681242 chr18:28681278-28681286
23	POLR2A	chr18:28681063-28681739	HepG2	liver:	n/a	n/a
24	POLR2A	chr18:28680810-28682070	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr18:28679933-28682875	H1-hESC	embryonic stem cell:	n/a	n/a
26	CHD2	chr18:28680834-28681390	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr18:28681076-28682073	HL-60	blood:	n/a	n/a
28	POLR2A	chr18:28680938-28682628	H1-neurons	neurons:	n/a	n/a
29	MAX	chr18:28681143-28681688	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr18:28680643-28682543	H1-hESC	embryonic stem cell:	n/a	n/a
31	BHLHE40	chr18:28680962-28681342	GM12878	blood:	n/a	n/a
32	MAX	chr18:28681159-28681667	A549	lung:	n/a	n/a
33	TAF1	chr18:28681164-28681733	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr18:28680220-28682702	K562	blood:	n/a	n/a
35	TAL1	chr18:28681081-28681352	K562	blood:	n/a	n/a
36	POLR2A	chr18:28681234-28681774	ECC-1	luminal epithelium:	n/a	n/a
37	TAF7	chr18:28681114-28681527	H1-hESC	embryonic stem cell:	n/a	n/a
38	TAF1	chr18:28681155-28682154	HepG2	liver:	n/a	n/a
39	POLR2A	chr18:28681209-28681437	GM12891	blood:	n/a	n/a
40	RUNX3	chr18:28680944-28681344	GM12878	blood:	n/a	n/a
41	FOXA2	chr18:28681095-28681408	HepG2	liver:	n/a	n/a
42	POLR2A	chr18:28681017-28681692	HepG2	liver:	n/a	n/a
43	POLR2A	chr18:28680717-28683015	HepG2	liver:	n/a	n/a
44	POLR2A	chr18:28681247-28681739	MCF-7	breast:	n/a	n/a
45	TBP	chr18:28680875-28681324	HepG2	liver:	n/a	n/a
46	CREB1	chr18:28681049-28682684	HepG2	liver:	n/a	n/a
47	TBP	chr18:28680567-28682783	K562	blood:	n/a	n/a
48	TEAD4	chr18:28681197-28681670	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr18:28681079-28681520	MCF-7	breast:	n/a	n/a
50	SIN3A	chr18:28680576-28682705	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:28680816..28682711-chr18:29076315..29078384,2	K562	blood:
2	chr18:28663717..28665312-chr18:28679601..28681471,2	K562	blood:
3	chr11:65265695..65267786-chr18:28681110..28682846,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265888	TF binding region
ENSG00000266521	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000046604	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388313	chr18:28583296-28693160	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530788	chr18:28596461-28751891	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3384119	chr18:28679654-28682652	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28678800-28682400	Active TSS	Duodenum Mucosa	Duodenum
2	chr18:28679200-28682800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr18:28679800-28682400	Active TSS	Esophagus	oesophagus
4	chr18:28679800-28682800	Active TSS	Rectal Smooth Muscle	rectum
5	chr18:28680000-28682600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr18:28680000-28682600	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr18:28680000-28682800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr18:28680000-28682800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr18:28680200-28682000	Bivalent/Poised TSS	Fetal Stomach	stomach
10	chr18:28680200-28682400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr18:28680200-28682400	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr18:28680200-28682600	Active TSS	Colon Smooth Muscle	Colon
13	chr18:28680200-28682600	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr18:28680200-28682600	Active TSS	Placenta Amnion	Placenta Amnion
15	chr18:28680200-28682800	Active TSS	H1 Cell Line	embryonic stem cell
16	chr18:28680200-28682800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr18:28680200-28682800	Active TSS	Colonic Mucosa	Colon
18	chr18:28680200-28683000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr18:28680400-28682000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr18:28680400-28682200	Active TSS	Placenta	Placenta
21	chr18:28680400-28682400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr18:28680400-28682400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr18:28680400-28682400	Bivalent/Poised TSS	Fetal Thymus	thymus
24	chr18:28680400-28682400	Active TSS	Pancreas	Pancrea
25	chr18:28680400-28682400	Active TSS	Sigmoid Colon	Sigmoid Colon
26	chr18:28680400-28682400	Active TSS	Stomach Mucosa	stomach
27	chr18:28680400-28682600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr18:28680400-28682600	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr18:28680400-28682600	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr18:28680400-28682600	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr18:28680400-28682600	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr18:28680400-28682600	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr18:28680400-28682600	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr18:28680400-28682600	Active TSS	Brain Anterior Caudate	brain
35	chr18:28680400-28682600	Active TSS	Right Ventricle	heart
36	chr18:28680400-28682800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr18:28680400-28682800	Active TSS	Fetal Intestine Large	intestine
38	chr18:28680400-28682800	Active TSS	Fetal Kidney	kidney
39	chr18:28680600-28681400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr18:28680600-28681800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr18:28680600-28681800	Active TSS	Fetal Heart	heart
42	chr18:28680600-28682200	Active TSS	HMEC	breast
43	chr18:28680600-28682400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr18:28680600-28682400	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr18:28680600-28682400	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr18:28680600-28682400	Bivalent/Poised TSS	Thymus	Thymus
47	chr18:28680600-28682400	Active TSS	A549	lung
48	chr18:28680600-28682400	Active TSS	NHEK	skin
49	chr18:28680600-28682600	Active TSS	Brain Angular Gyrus	brain
50	chr18:28680600-28682600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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