Variant report

Variant	rs559011039
Chromosome Location	chr2:55844144-55844145
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:221)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:221 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr2:55844126-55845422	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:55843883-55846194	K562	blood:	n/a	n/a
3	IRF1	chr2:55843623-55844175	K562	blood:	n/a	chr2:55843809-55843823 chr2:55843808-55843820 chr2:55843808-55843820
4	POLR2A	chr2:55843823-55845589	ECC-1	luminal epithelium:	n/a	n/a
5	STAT5A	chr2:55844038-55845386	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:55844100-55845316	MCF-7	breast:	n/a	n/a
7	TAF1	chr2:55844047-55845260	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:55843886-55845373	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr2:55843571-55846136	GM12892	blood:	n/a	n/a
10	SIN3A	chr2:55843617-55846240	GM12878	blood:	n/a	chr2:55845166-55845176
11	YY1	chr2:55844135-55845391	GM12891	blood:	n/a	n/a
12	REST	chr2:55844072-55844291	Hela-S3	cervix:	n/a	n/a
13	MYC	chr2:55843605-55844149	MCF10A-Er-Src	breast:	n/a	n/a
14	FOXA1	chr2:55843585-55844195	HepG2	liver:	n/a	chr2:55843932-55843944
15	YY1	chr2:55843974-55845446	GM12878	blood:	n/a	n/a
16	TAF1	chr2:55843902-55845498	K562	blood:	n/a	n/a
17	TCF7L2	chr2:55843595-55845209	Hela-S3	cervix:	n/a	n/a
18	YY1	chr2:55843891-55846225	SK-N-SH	brain:	n/a	n/a
19	YY1	chr2:55843887-55845290	SK-N-SH	brain:	n/a	n/a
20	SMARCC1	chr2:55843646-55845378	Hela-S3	cervix:	n/a	n/a
21	PML	chr2:55843531-55846089	GM12878	blood:	n/a	n/a
22	TBP	chr2:55843791-55845358	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr2:55843683-55846210	Hela-S3	cervix:	n/a	n/a
24	TBP	chr2:55843543-55845475	HepG2	liver:	n/a	n/a
25	POLR2A	chr2:55843919-55845340	ECC-1	luminal epithelium:	n/a	n/a
26	SIN3AK20	chr2:55843632-55846368	MCF-7	breast:	n/a	n/a
27	POLR2A	chr2:55843853-55844238	SK-N-SH	brain:	n/a	n/a
28	ZNF143	chr2:55843925-55844299	H1-hESC	embryonic stem cell:	n/a	n/a
29	HEY1	chr2:55843664-55846223	HepG2	liver:	n/a	n/a
30	YY1	chr2:55844081-55846207	A549	lung:	n/a	n/a
31	POLR2A	chr2:55843453-55846870	H1-hESC	embryonic stem cell:	n/a	n/a
32	REST	chr2:55844008-55844278	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr2:55843622-55846213	GM12891	blood:	n/a	n/a
34	MYBL2	chr2:55843541-55844349	HepG2	liver:	n/a	n/a
35	MXI1	chr2:55843595-55844180	Hela-S3	cervix:	n/a	n/a
36	CHD2	chr2:55843634-55846218	Hela-S3	cervix:	n/a	n/a
37	YY1	chr2:55843901-55845412	GM12878	blood:	n/a	n/a
38	POLR2A	chr2:55843522-55846253	GM12892	blood:	n/a	n/a
39	CCNT2	chr2:55844124-55845338	K562	blood:	n/a	n/a
40	POLR2A	chr2:55843548-55846185	GM12891	blood:	n/a	n/a
41	POLR2A	chr2:55843932-55846130	K562	blood:	n/a	n/a
42	MAZ	chr2:55843638-55845275	Hela-S3	cervix:	n/a	n/a
43	SIN3AK20	chr2:55843691-55846223	A549	lung:	n/a	n/a
44	POLR2A	chr2:55843629-55846191	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr2:55843943-55844289	SK-N-SH	brain:	n/a	n/a
46	CEBPB	chr2:55844075-55845120	HepG2	liver:	n/a	n/a
47	FOXA1	chr2:55843665-55844190	HepG2	liver:	n/a	chr2:55843932-55843944
48	YY1	chr2:55843983-55845217	HepG2	liver:	n/a	n/a
49	TAF1	chr2:55843888-55844268	GM12891	blood:	n/a	n/a
50	WRNIP1	chr2:55843598-55844419	GM12878	blood:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55496021..55497900-chr2:55843389..55845266,2	K562	blood:
2	chr2:55746181..55748765-chr2:55843177..55845713,3	MCF-7	breast:
3	chr15:52859559..52861665-chr2:55842687..55845255,2	MCF-7	breast:
4	chr2:55843362..55845607-chr2:55918078..55921710,3	K562	blood:
5	chr2:55841795..55844862-chr2:55919047..55922552,3	K562	blood:
6	chr2:55643936..55648492-chr2:55843198..55848689,6	K562	blood:
7	chr2:55494631..55497013-chr2:55842868..55845390,2	MCF-7	breast:
8	chr2:55843912..55844474-chrX:27481115..27481634,2	Hela-S3	cervix:
9	chr2:55843805..55846748-chr2:55896170..55899222,4	MCF-7	breast:
10	chr2:55496021..55498315-chr2:55843389..55845953,2	K562	blood:
11	chr10:99051546..99052354-chr2:55843946..55844595,2	Hela-S3	cervix:
12	chr2:55273795..55276620-chr2:55843969..55846667,2	K562	blood:
13	chr17:27052759..27053541-chr2:55843996..55844983,2	Hela-S3	cervix:
14	chr2:55644452..55648722-chr2:55843350..55848689,7	K562	blood:
15	chr2:55458277..55462347-chr2:55843080..55846218,4	K562	blood:
16	chr17:57914014..57916719-chr2:55842770..55844822,2	MCF-7	breast:
17	chr2:55507639..55510296-chr2:55843126..55844712,2	K562	blood:
18	chr2:55459912..55461600-chr2:55842449..55844888,2	K562	blood:
19	chr2:55508376..55510742-chr2:55843787..55846796,4	K562	blood:

No data

Variant related genes	Relation type
SMEK2	TF binding region
ENSG00000272606	TF binding region
ENSG00000162994	Chromatin interaction
ENSG00000128989	Chromatin interaction
ENSG00000143947	Chromatin interaction
ENSG00000085760	Chromatin interaction
ENSG00000160602	Chromatin interaction
ENSG00000138035	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000162997	Chromatin interaction
ENSG00000163001	Chromatin interaction
ENSG00000160606	Chromatin interaction
ENSG00000115355	Chromatin interaction
ENSG00000224960	Chromatin interaction
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	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
3	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv829430	chr2:55843689-55844381	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	15 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	chr2:55842400-55846200	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr2:55842400-55846200	Active TSS	NH-A	brain
3	chr2:55842400-55846400	Active TSS	HSMMtube	muscle
4	chr2:55842400-55846400	Active TSS	NHLF	lung
5	chr2:55842600-55846200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:55842600-55846200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr2:55842600-55846200	Active TSS	A549	lung
8	chr2:55842600-55846200	Active TSS	K562	blood
9	chr2:55842600-55846400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:55842600-55846400	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr2:55842600-55846400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:55842600-55846400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:55842600-55846400	Active TSS	Pancreas	Pancrea
14	chr2:55842600-55846400	Active TSS	Psoas Muscle	Psoas
15	chr2:55842600-55846800	Active TSS	H1 Cell Line	embryonic stem cell
16	chr2:55842800-55844200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:55842800-55845400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:55842800-55846000	Active TSS	Liver	Liver
19	chr2:55842800-55846200	Active TSS	Brain Hippocampus Middle	brain
20	chr2:55842800-55846200	Active TSS	Stomach Smooth Muscle	stomach
21	chr2:55842800-55846200	Active TSS	GM12878-XiMat	blood
22	chr2:55842800-55846200	Active TSS	Hela-S3	cervix
23	chr2:55842800-55846200	Active TSS	HMEC	breast
24	chr2:55842800-55846400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:55842800-55846400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:55842800-55846400	Active TSS	Fetal Intestine Large	intestine
27	chr2:55842800-55846400	Active TSS	Fetal Kidney	kidney
28	chr2:55842800-55846400	Active TSS	HSMM	muscle
29	chr2:55842800-55846800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:55842800-55847800	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr2:55843000-55845200	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr2:55843000-55846200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:55843000-55846200	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr2:55843000-55846200	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr2:55843000-55846200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:55843000-55846200	Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr2:55843000-55846200	Active TSS	Muscle Satellite Cultured Cells	--
38	chr2:55843000-55846200	Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr2:55843000-55846200	Active TSS	Brain Cingulate Gyrus	brain
40	chr2:55843000-55846200	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr2:55843000-55846200	Active TSS	NHDF-Ad	bronchial
42	chr2:55843000-55846200	Active TSS	NHEK	skin
43	chr2:55843000-55846400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:55843000-55846400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:55843000-55846400	Active TSS	Colonic Mucosa	Colon
46	chr2:55843000-55846400	Active TSS	Fetal Intestine Small	intestine
47	chr2:55843000-55846400	Active TSS	Left Ventricle	heart
48	chr2:55843000-55846400	Active TSS	Ovary	ovary
49	chr2:55843000-55846400	Active TSS	Right Atrium	heart
50	chr2:55843000-55846600	Active TSS	ES-I3 Cell Line	embryonic stem cell

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