Variant report

Variant	rs55676306
Chromosome Location	chr2:56220104-56220105
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	POLR2A	chr2:56219575-56220233	HUVEC	blood vessel:	n/a	n/a
2	SMC3	chr2:56219303-56220119	Hela-S3	cervix:	n/a	n/a
3	GATA2	chr2:56219215-56220138	HUVEC	blood vessel:	n/a	chr2:56219798-56219807 chr2:56219789-56219806 chr2:56219798-56219808 chr2:56219800-56219807 chr2:56219793-56219814 chr2:56219743-56219756 chr2:56219797-56219811 chr2:56219800-56219810
4	FOSL2	chr2:56219519-56220185	SK-N-SH	brain:	n/a	chr2:56219826-56219833 chr2:56219825-56219833
5	TEAD4	chr2:56219311-56220205	A549	lung:	n/a	n/a
6	EP300	chr2:56219221-56220328	SK-N-SH	brain:	n/a	n/a
7	TEAD4	chr2:56219191-56220265	SK-N-SH	brain:	n/a	n/a
8	RXRA	chr2:56219328-56220213	SK-N-SH	brain:	n/a	chr2:56219343-56219365 chr2:56219634-56219656
9	POLR2A	chr2:56218058-56220673	HUVEC	blood vessel:	n/a	n/a
10	SP1	chr2:56219273-56220250	A549	lung:	n/a	n/a
11	FOSL2	chr2:56219312-56220394	A549	lung:	n/a	chr2:56219826-56219833 chr2:56219825-56219833
12	PBX3	chr2:56219239-56220159	SK-N-SH	brain:	n/a	n/a
13	FOXA2	chr2:56219448-56220112	A549	lung:	n/a	chr2:56219681-56219693 chr2:56219505-56219517
14	BCL3	chr2:56219437-56220124	A549	lung:	n/a	n/a
15	JUND	chr2:56219386-56220370	Hela-S3	cervix:	n/a	chr2:56219826-56219833 chr2:56219825-56219833
16	JUND	chr2:56219352-56220242	SK-N-SH	brain:	n/a	chr2:56219826-56219833 chr2:56219825-56219833
17	TBP	chr2:56219236-56220267	Hela-S3	cervix:	n/a	n/a
18	ATF3	chr2:56219488-56220127	A549	lung:	n/a	n/a
19	PBX3	chr2:56219143-56220227	SK-N-SH	brain:	n/a	n/a
20	TCF12	chr2:56219215-56220363	A549	lung:	n/a	n/a
21	TEAD4	chr2:56219361-56220190	SK-N-SH	brain:	n/a	n/a
22	JUN	chr2:56219321-56220233	HUVEC	blood vessel:	n/a	chr2:56219826-56219833 chr2:56219825-56219833
23	MAX	chr2:56219434-56220115	A549	lung:	n/a	n/a
24	CEBPB	chr2:56219395-56220252	Hela-S3	cervix:	n/a	n/a
25	CEBPB	chr2:56219371-56220182	A549	lung:	n/a	n/a
26	STAT3	chr2:56219519-56220155	MCF10A-Er-Src	breast:	n/a	chr2:56219994-56220002
27	FOSL2	chr2:56219339-56220260	SK-N-SH	brain:	n/a	chr2:56219826-56219833 chr2:56219825-56219833
28	EP300	chr2:56219248-56220203	A549	lung:	n/a	n/a
29	GATA3	chr2:56219237-56220278	SK-N-SH	brain:	n/a	chr2:56219798-56219807 chr2:56219789-56219806 chr2:56219798-56219808 chr2:56219800-56219807 chr2:56219793-56219814 chr2:56219743-56219756 chr2:56219800-56219810
30	REST	chr2:56219431-56220135	A549	lung:	n/a	n/a
31	TEAD4	chr2:56219458-56220104	A549	lung:	n/a	n/a
32	MAX	chr2:56219547-56220140	SK-N-SH	brain:	n/a	n/a
33	MAFK	chr2:56219383-56220242	Hela-S3	cervix:	n/a	chr2:56219593-56219604
34	MAX	chr2:56219366-56220265	A549	lung:	n/a	n/a
35	JUND	chr2:56218944-56220314	SK-N-SH	brain:	n/a	chr2:56219826-56219833 chr2:56219825-56219833
36	POLR2A	chr2:56219411-56220592	HUVEC	blood vessel:	n/a	n/a
37	ELF1	chr2:56219480-56220180	SK-N-SH	brain:	n/a	n/a
38	STAT1	chr2:56219587-56220192	Hela-S3	cervix:	n/a	chr2:56219994-56220002
39	CHD2	chr2:56219412-56220106	Hela-S3	cervix:	n/a	n/a
40	RFX5	chr2:56219236-56220327	Hela-S3	cervix:	n/a	n/a
41	MYC	chr2:56219641-56220154	MCF10A-Er-Src	breast:	n/a	n/a
42	EP300	chr2:56219136-56220322	A549	lung:	n/a	n/a
43	GATA3	chr2:56219088-56220328	SK-N-SH	brain:	n/a	chr2:56219798-56219807 chr2:56219789-56219806 chr2:56219798-56219808 chr2:56219800-56219807 chr2:56219793-56219814 chr2:56219743-56219756 chr2:56219800-56219810
44	STAT3	chr2:56219406-56220206	Hela-S3	cervix:	n/a	chr2:56219994-56220002
45	EP300	chr2:56219262-56220354	SK-N-SH	brain:	n/a	n/a
46	BCL3	chr2:56219311-56220202	A549	lung:	n/a	n/a
47	POLR2A	chr2:56219107-56220630	HUVEC	blood vessel:	n/a	n/a
48	CEBPB	chr2:56219618-56220127	IMR90	lung:	n/a	n/a
49	MEF2A	chr2:56219477-56220208	SK-N-SH	brain:	n/a	n/a
50	FOS	chr2:56219632-56220132	MCF10A-Er-Src	breast:	n/a	chr2:56219826-56219833 chr2:56219825-56219833

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:56220104-56220154	SK-N-SH	brain:	n/a
2	chr2:56220104-56220154	A549	lung:	n/a
3	chr2:56220104-56220154	RPTEC	kidney:	n/a
4	chr2:56220104-56220154	HRE	kidney:	n/a
5	chr2:56220104-56220154	T-47D	breast:	n/a
6	chr2:56220104-56220154	HCPEpiC	choroid plexus:	n/a
7	chr2:56220104-56220154	AG10803	skin:	n/a
8	chr2:56220104-56220154	Hela-S3	cervix:	n/a
9	chr2:56220104-56220154	HCF	heart:	n/a
10	chr2:56220104-56220154	ECC-1	luminal epithelium:	n/a
11	chr2:56220104-56220154	MCF10A-Er-Src	breast:	n/a
12	chr2:56220104-56220154	LNCaP	prostate:	n/a
13	chr2:56220104-56220154	HL-60	blood:	n/a
14	chr2:56220104-56220154	U87	brain:	n/a
15	chr2:56220104-56220154	SAEC	small airway:	n/a
16	chr2:56220104-56220154	BE2_C	brain:	n/a
17	chr2:56220104-56220154	IMR90	lung:	fetal
18	chr2:56220104-56220154	GM06990	blood:	n/a
19	chr2:56220104-56220154	ovcar-3	ovarian:	n/a
20	chr2:56220104-56220154	AG09309	skin:	n/a
21	chr2:56220104-56220154	NB4	blood:	n/a
22	chr2:56220104-56220154	HPAEpiC	pulmonary alveolar:	n/a
23	chr2:56220104-56220154	MCF-7	breast:	n/a
24	chr2:56220104-56220154	H1-hESC	embryonic stem cell:	embryo
25	chr2:56220104-56220154	AG09319	gingival:	n/a
26	chr2:56220104-56220154	SKMC	muscle:	n/a
27	chr2:56220104-56220154	GM12878	blood:	n/a
28	chr2:56220104-56220154	SK-N-MC	brain:	n/a
29	chr2:56220104-56220154	HRCEpiC	kidney:	n/a
30	chr2:56220104-56220154	PrEC	prostate:	n/a
31	chr2:56220104-56220154	BJ	skin:	n/a
32	chr2:56220104-56220154	HRPEpiC	eye:	n/a
33	chr2:56220104-56220154	NHDF-neo	bronchial:	n/a
34	chr2:56220104-56220154	AoSMC	blood vessel:	n/a
35	chr2:56220104-56220154	GM19239	blood:	n/a
36	chr2:56220104-56220154	K562	blood:	n/a
37	chr2:56220104-56220154	CMK	blood:	n/a
38	chr2:56220104-56220154	HEEpiC	esophagus:	n/a
39	chr2:56220104-56220154	GM12892	blood:	n/a
40	chr2:56220104-56220154	ProgFib	skin:	n/a
41	chr2:56220104-56220154	PFSK-1	brain:	n/a
42	chr2:56220104-56220154	HepG2	liver:	n/a
43	chr2:56220104-56220154	Jurkat	blood:	n/a
44	chr2:56220104-56220154	AG04449	skin:	fetal
45	chr2:56220104-56220154	HMEC	breast:	n/a
46	chr2:56220104-56220154	HCM	heart:	n/a
47	chr2:56220104-56220154	NT2-D1	testis:	n/a
48	chr2:56220104-56220154	Hepatocyte	liver:	n/a
49	chr2:56220104-56220154	SK-N-SH_RA	brain:	n/a
50	chr2:56220104-56220154	HAEpiC	amniotic membrane:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:56214240..56215835-chr2:56218212..56220191,2	MCF-7	breast:

Variant related genes	Relation type
MIR216A	TF binding region
MIR216A	CpG island

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10518794	0.89[EUR][1000 genomes]
rs55749412	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55811442	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55845766	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55912959	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56058144	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56195925	0.95[EUR][1000 genomes]
rs56309449	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56412571	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72813864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72813868	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72813873	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72813875	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72813877	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72813878	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72813879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72813880	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72813884	0.95[EUR][1000 genomes]
rs72813888	0.95[EUR][1000 genomes]
rs72813889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72813894	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72813900	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72813901	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72813902	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72815903	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72815905	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72815906	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72815907	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72815909	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72815910	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72815912	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72815915	0.89[AMR][1000 genomes]
rs7600678	0.95[EUR][1000 genomes]

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	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56217000-56223200	Enhancers	HUVEC	blood vessel
2	chr2:56217200-56222800	Weak transcription	Pancreas	Pancrea
3	chr2:56218000-56220400	Enhancers	HSMMtube	muscle
4	chr2:56218000-56222400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:56218400-56221000	Enhancers	Hela-S3	cervix
6	chr2:56218400-56221200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr2:56218400-56222200	Enhancers	HSMM	muscle
8	chr2:56218400-56223000	Enhancers	Muscle Satellite Cultured Cells	--
9	chr2:56218600-56220600	Enhancers	NH-A	brain
10	chr2:56218600-56221200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:56218800-56220400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:56218800-56220600	Enhancers	NHDF-Ad	bronchial
13	chr2:56218800-56220600	Enhancers	Osteobl	bone
14	chr2:56219000-56221000	Enhancers	NHLF	lung
15	chr2:56219000-56221200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:56219000-56221200	Enhancers	HMEC	breast
17	chr2:56219600-56220200	Enhancers	Adipose Nuclei	Adipose
18	chr2:56219600-56220200	Enhancers	Aorta	Aorta
19	chr2:56219600-56220400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:56219600-56220600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:56219600-56222000	Enhancers	Fetal Stomach	stomach
22	chr2:56219800-56220200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:56219800-56220200	Enhancers	Ovary	ovary
24	chr2:56220000-56220400	Flanking Active TSS	A549	lung
25	chr2:56220000-56220600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:56220000-56222000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:56220000-56222200	Weak transcription	Colon Smooth Muscle	Colon

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