Variant report

Variant	rs542127326
Chromosome Location	chr4:53525557-53525558
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	MYC	chr4:53525553-53525572	MCF-7	breast:	n/a	n/a
2	YY1	chr4:53525225-53525718	HCT-116	colon:	n/a	chr4:53525406-53525417 chr4:53525347-53525355 chr4:53525344-53525354 chr4:53525345-53525353 chr4:53525343-53525355 chr4:53525344-53525366
3	YY1	chr4:53525080-53525692	H1-hESC	embryonic stem cell:	n/a	chr4:53525129-53525143 chr4:53525406-53525417 chr4:53525347-53525355 chr4:53525344-53525354 chr4:53525345-53525353 chr4:53525105-53525116 chr4:53525343-53525355 chr4:53525344-53525366
4	CTCF	chr4:53525520-53525670	AG04449	skin:	n/a	n/a
5	POLR2A	chr4:53525163-53525966	A549	lung:	n/a	n/a
6	POLR2A	chr4:53525143-53525860	HUVEC	blood vessel:	n/a	n/a
7	YY1	chr4:53524914-53526431	SK-N-SH	brain:	n/a	chr4:53525129-53525143 chr4:53525406-53525417 chr4:53526019-53526038 chr4:53525944-53525955 chr4:53525347-53525355 chr4:53525344-53525354 chr4:53525345-53525353 chr4:53525866-53525880 chr4:53525105-53525116 chr4:53525869-53525883 chr4:53525343-53525355 chr4:53525344-53525366
8	CHD2	chr4:53525272-53526188	Hela-S3	cervix:	n/a	chr4:53526060-53526070
9	POLR2A	chr4:53525487-53525789	Hela-S3	cervix:	n/a	n/a
10	YY1	chr4:53524890-53526329	HepG2	liver:	n/a	chr4:53525129-53525143 chr4:53525406-53525417 chr4:53526019-53526038 chr4:53525944-53525955 chr4:53525347-53525355 chr4:53525344-53525354 chr4:53525345-53525353 chr4:53525866-53525880 chr4:53525105-53525116 chr4:53525869-53525883 chr4:53525343-53525355 chr4:53525344-53525366
11	YY1	chr4:53525124-53525794	ECC-1	luminal epithelium:	n/a	chr4:53525129-53525143 chr4:53525406-53525417 chr4:53525347-53525355 chr4:53525344-53525354 chr4:53525345-53525353 chr4:53525343-53525355 chr4:53525344-53525366
12	MAX	chr4:53525272-53525839	K562	blood:	n/a	n/a
13	POLR2A	chr4:53524888-53525834	HEK293	kidney:	n/a	n/a
14	YY1	chr4:53525082-53525802	ECC-1	luminal epithelium:	n/a	chr4:53525129-53525143 chr4:53525406-53525417 chr4:53525347-53525355 chr4:53525344-53525354 chr4:53525345-53525353 chr4:53525105-53525116 chr4:53525343-53525355 chr4:53525344-53525366
15	E2F6	chr4:53525462-53525675	K562	blood:	n/a	n/a
16	POLR2A	chr4:53524897-53526532	GM18505	blood:	n/a	n/a
17	HCFC1	chr4:53524899-53525730	K562	blood:	n/a	n/a
18	MAX	chr4:53525134-53526595	HepG2	liver:	n/a	n/a
19	RCOR1	chr4:53525241-53526386	GM12878	blood:	n/a	n/a
20	POLR2A	chr4:53525239-53525778	K562	blood:	n/a	n/a
21	TAF1	chr4:53524882-53526269	H1-hESC	embryonic stem cell:	n/a	n/a
22	IRF1	chr4:53525239-53525694	K562	blood:	n/a	n/a
23	MAX	chr4:53525119-53526581	NB4	blood:	n/a	n/a
24	TCF12	chr4:53525097-53526325	ECC-1	luminal epithelium:	n/a	chr4:53526094-53526101
25	POLR2A	chr4:53525127-53525896	Gliobla	brain:	n/a	n/a
26	TBP	chr4:53525203-53526411	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAX	chr4:53525170-53526582	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr4:53525508-53525753	GM12891	blood:	n/a	n/a
29	POLR2A	chr4:53525168-53525837	Raji	blood:	n/a	n/a
30	POLR2A	chr4:53525092-53526504	GM18526	blood:	n/a	n/a
31	POLR2A	chr4:53525112-53526534	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr4:53525249-53525769	SK-N-SH	brain:	n/a	n/a
33	ZBTB7A	chr4:53524695-53525998	ECC-1	luminal epithelium:	n/a	n/a
34	MYC	chr4:53525189-53525915	MCF-7	breast:	n/a	n/a
35	POLR2A	chr4:53524926-53526430	GM12892	blood:	n/a	n/a
36	ELF1	chr4:53525425-53526049	GM12878	blood:	n/a	n/a
37	POLR2A	chr4:53525215-53526816	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr4:53525088-53525859	PFSK-1	brain:	n/a	n/a
39	POLR2A	chr4:53525193-53525853	HUVEC	blood vessel:	n/a	n/a
40	SMARCB1	chr4:53524913-53526553	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr4:53525193-53526127	GM10847	blood:	n/a	n/a
42	TBP	chr4:53525130-53526489	K562	blood:	n/a	n/a
43	TAF1	chr4:53525094-53526011	HepG2	liver:	n/a	n/a
44	YY1	chr4:53524832-53526303	GM12892	blood:	n/a	chr4:53525129-53525143 chr4:53525406-53525417 chr4:53526019-53526038 chr4:53525944-53525955 chr4:53525347-53525355 chr4:53525344-53525354 chr4:53525345-53525353 chr4:53525866-53525880 chr4:53525105-53525116 chr4:53525869-53525883 chr4:53525343-53525355 chr4:53525344-53525366
45	POLR2A	chr4:53524885-53526430	H1-hESC	embryonic stem cell:	n/a	n/a
46	MXI1	chr4:53525140-53526534	HepG2	liver:	n/a	n/a
47	POLR2A	chr4:53525517-53525785	H1-hESC	embryonic stem cell:	n/a	n/a
48	ZBTB7A	chr4:53524795-53525639	ECC-1	luminal epithelium:	n/a	n/a
49	TAF1	chr4:53525166-53525599	H1-neurons	neurons:	n/a	n/a
50	MAZ	chr4:53524810-53526566	K562	blood:	n/a	chr4:53525015-53525025

No.	Distal block	Cell Line	Cell type
1	chr4:53525430..53527688-chr4:53726700..53729187,4	MCF-7	breast:
2	chr17:5389478..5390355-chr4:53525501..53526123,2	Hela-S3	cervix:
3	chr4:53523849..53530507-chr4:53576531..53584814,17	K562	blood:
4	chr4:53524001..53527558-chr4:53577308..53580194,4	MCF-7	breast:
5	chr4:53519355..53522911-chr4:53523707..53526726,6	MCF-7	breast:
6	chr4:53523914..53526614-chr4:53586643..53588754,3	MCF-7	breast:
7	chr4:53492777..53495734-chr4:53523846..53526517,2	K562	blood:
8	chr4:53523968..53528771-chr4:53576572..53580241,9	MCF-7	breast:
9	chr4:53515781..53522890-chr4:53523068..53527068,15	MCF-7	breast:
10	chr4:53522503..53529252-chr4:53576629..53581800,10	K562	blood:

Variant related genes	Relation type
USP46	TF binding region
USP46-AS1	TF binding region
ENSG00000167842	Chromatin interaction
ENSG00000072849	Chromatin interaction
ENSG00000109189	Chromatin interaction
ENSG00000226950	Chromatin interaction
ENSG00000264585	Chromatin interaction
ENSG00000212588	Chromatin interaction
ENSG00000248375	Chromatin interaction
ENSG00000128045	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1000931	chr4:53420849-53689319	Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537093	chr4:53420849-53689319	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv948860	chr4:53421172-53675549	Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv2754049	chr4:53454272-53539672	Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv524494	chr4:53459620-53582065	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	esv3344129	chr4:53524220-53527168	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53523000-53527000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:53523600-53526400	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr4:53523800-53526200	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr4:53523800-53526400	Active TSS	Brain Angular Gyrus	brain
5	chr4:53523800-53526600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr4:53523800-53526600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:53523800-53526600	Active TSS	NHLF	lung
8	chr4:53523800-53526800	Active TSS	NHDF-Ad	bronchial
9	chr4:53523800-53527200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:53524000-53526200	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr4:53524000-53526200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:53524000-53526200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:53524000-53526200	Active TSS	Rectal Smooth Muscle	rectum
14	chr4:53524000-53526800	Active TSS	Aorta	Aorta
15	chr4:53524200-53526000	Active TSS	Primary T cells from cord blood	blood
16	chr4:53524200-53526000	Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr4:53524200-53526200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:53524200-53526400	Active TSS	Fetal Kidney	kidney
19	chr4:53524200-53526600	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr4:53524200-53526600	Active TSS	HSMMtube	muscle
21	chr4:53524400-53526600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:53524400-53526600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr4:53524400-53526600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:53524600-53525800	Active TSS	Brain Germinal Matrix	brain
25	chr4:53524600-53525800	Bivalent/Poised TSS	Thymus	Thymus
26	chr4:53524600-53526000	Active TSS	Fetal Stomach	stomach
27	chr4:53524600-53526200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:53524600-53526200	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr4:53524600-53526200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr4:53524600-53526200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr4:53524600-53526200	Active TSS	Fetal Heart	heart
32	chr4:53524600-53526400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr4:53524600-53526400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr4:53524600-53526400	Active TSS	Placenta Amnion	Placenta Amnion
35	chr4:53524600-53526600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr4:53524600-53526600	Active TSS	Colonic Mucosa	Colon
37	chr4:53524600-53526600	Active TSS	Esophagus	oesophagus
38	chr4:53524600-53526600	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr4:53524600-53526600	Active TSS	Gastric	stomach
40	chr4:53524600-53526600	Active TSS	Ovary	ovary
41	chr4:53524600-53526600	Active TSS	Psoas Muscle	Psoas
42	chr4:53524600-53526800	Active TSS	Brain Substantia Nigra	brain
43	chr4:53524600-53526800	Active TSS	HMEC	breast
44	chr4:53524800-53525800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr4:53524800-53525800	Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr4:53524800-53526000	Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr4:53524800-53526000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:53524800-53526000	Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr4:53524800-53526000	Active TSS	Fetal Muscle Trunk	muscle
50	chr4:53524800-53526200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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