Variant report

Variant	rs546499840
Chromosome Location	chr15:77711911-77711912
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	POLR2A	chr15:77711788-77714120	GM12878	blood:	n/a	n/a
2	CHD2	chr15:77711804-77712033	GM12878	blood:	n/a	n/a
3	E2F6	chr15:77711687-77713457	K562	blood:	n/a	chr15:77712417-77712427 chr15:77712728-77712737
4	POLR2A	chr15:77711874-77713573	HUVEC	blood vessel:	n/a	n/a
5	ZBTB7A	chr15:77711907-77712059	HepG2	liver:	n/a	n/a
6	SIN3AK20	chr15:77711369-77712093	SK-N-SH	brain:	n/a	n/a
7	RUNX3	chr15:77711513-77711915	GM12878	blood:	n/a	n/a
8	YY1	chr15:77711846-77712093	K562	blood:	n/a	chr15:77712001-77712015
9	CTCF	chr15:77711893-77712116	K562	blood:	n/a	chr15:77711917-77711930
10	TAF1	chr15:77711847-77712035	SK-N-SH	brain:	n/a	n/a
11	TAF1	chr15:77711814-77712929	K562	blood:	n/a	n/a
12	RFX5	chr15:77711201-77712051	Hela-S3	cervix:	n/a	n/a
13	MAZ	chr15:77711447-77713888	GM12878	blood:	n/a	chr15:77711944-77711954 chr15:77712740-77712750
14	EGR1	chr15:77711609-77712285	K562	blood:	n/a	chr15:77712082-77712096 chr15:77711945-77711955 chr15:77711647-77711660
15	SIN3AK20	chr15:77711730-77712727	PANC-1	pancreas:	n/a	n/a
16	MAX	chr15:77711877-77712117	K562	blood:	n/a	chr15:77711944-77711954
17	CTCF	chr15:77711895-77712125	MCF-7	breast:	n/a	chr15:77711917-77711930
18	RUNX3	chr15:77711514-77713773	GM12878	blood:	n/a	n/a
19	JUND	chr15:77711863-77713831	K562	blood:	n/a	chr15:77711921-77711932 chr15:77712726-77712735
20	ELF1	chr15:77711519-77712921	GM12878	blood:	n/a	chr15:77712419-77712428 chr15:77712001-77712013 chr15:77712362-77712371 chr15:77712737-77712749 chr15:77711858-77711867 chr15:77712415-77712427
21	ZNF143	chr15:77711746-77711938	K562	blood:	n/a	n/a
22	RAD21	chr15:77711907-77712120	K562	blood:	n/a	n/a
23	CHD2	chr15:77711455-77713966	Hela-S3	cervix:	n/a	chr15:77711545-77711555
24	POLR2A	chr15:77710728-77713515	IMR90	lung:	n/a	n/a
25	TAF1	chr15:77711776-77712057	H1-hESC	embryonic stem cell:	n/a	n/a
26	TBP	chr15:77711447-77712018	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr15:77711409-77713847	HepG2	liver:	n/a	n/a
28	EGR1	chr15:77711768-77712115	GM12878	blood:	n/a	chr15:77712082-77712096 chr15:77711945-77711955
29	EGR1	chr15:77711911-77712252	GM12878	blood:	n/a	chr15:77712082-77712096 chr15:77711945-77711955
30	MAZ	chr15:77711446-77713738	K562	blood:	n/a	chr15:77711944-77711954 chr15:77712740-77712750
31	ZBTB7A	chr15:77711340-77712620	ECC-1	luminal epithelium:	n/a	chr15:77712372-77712383 chr15:77711763-77711774 chr15:77712371-77712382
32	CTCF	chr15:77711840-77711990	HPF	lung:	n/a	chr15:77711917-77711930
33	RCOR1	chr15:77711809-77712008	Hela-S3	cervix:	n/a	n/a
34	BACH1	chr15:77711849-77713447	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr15:77711707-77712075	GM12878	blood:	n/a	n/a
36	POLR2A	chr15:77711735-77713947	K562	blood:	n/a	n/a
37	UBTF	chr15:77711276-77713516	K562	blood:	n/a	n/a
38	POLR2A	chr15:77711498-77713674	Hela-S3	cervix:	n/a	n/a
39	MAZ	chr15:77711510-77713691	HepG2	liver:	n/a	chr15:77711944-77711954 chr15:77712740-77712750
40	POLR2A	chr15:77711768-77713775	K562	blood:	n/a	n/a
41	BHLHE40	chr15:77711542-77711961	K562	blood:	n/a	n/a
42	YY1	chr15:77711761-77712987	HepG2	liver:	n/a	chr15:77711803-77711814 chr15:77712764-77712775 chr15:77712416-77712425 chr15:77712468-77712477 chr15:77712419-77712428 chr15:77712362-77712371 chr15:77712001-77712015
43	RAD21	chr15:77711621-77712529	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr15:77711800-77712183	K562	blood:	n/a	chr15:77711917-77711930
45	POLR2A	chr15:77711610-77712930	MCF-7	breast:	n/a	n/a
46	SMC3	chr15:77711175-77714043	Hela-S3	cervix:	n/a	chr15:77711935-77711945
47	POLR2A	chr15:77711833-77713021	ECC-1	luminal epithelium:	n/a	n/a
48	CTCF	chr15:77711860-77712010	HRE	kidney:	n/a	chr15:77711917-77711930
49	ZBTB7A	chr15:77711440-77712531	K562	blood:	n/a	chr15:77712372-77712383 chr15:77711763-77711774 chr15:77712371-77712382
50	CTCF	chr15:77711830-77712226	IMR90	lung:	n/a	chr15:77711917-77711930

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:77711899-77711949	ovcar-3	ovarian:	n/a
2	chr15:77711899-77711949	SK-N-SH	brain:	n/a
3	chr15:77711899-77711949	AoSMC	blood vessel:	n/a
4	chr15:77711899-77711949	BE2_C	brain:	n/a
5	chr15:77711899-77711949	HCT-116	colon:	n/a
6	chr15:77711899-77711949	HUVEC	blood vessel:	n/a
7	chr15:77711899-77711949	HEK293	kidney:	embryo
8	chr15:77711899-77711949	GM06990	blood:	n/a
9	chr15:77711899-77711949	AG04450	lung:	fetal
10	chr15:77711899-77711949	HIPEpiC	eye:	n/a
11	chr15:77711899-77711949	SK-N-SH_RA	brain:	n/a
12	chr15:77711899-77711949	HepG2	liver:	n/a
13	chr15:77711899-77711949	HPAEpiC	pulmonary alveolar:	n/a
14	chr15:77711899-77711949	SAEC	small airway:	n/a
15	chr15:77711899-77711949	NT2-D1	testis:	n/a
16	chr15:77711899-77711949	PrEC	prostate:	n/a
17	chr15:77711899-77711949	SKMC	muscle:	n/a
18	chr15:77711899-77711949	HCM	heart:	n/a
19	chr15:77711899-77711949	AG09309	skin:	n/a
20	chr15:77711899-77711949	ProgFib	skin:	n/a
21	chr15:77711899-77711949	GM12892	blood:	n/a
22	chr15:77711899-77711949	HL-60	blood:	n/a
23	chr15:77711899-77711949	SK-N-MC	brain:	n/a
24	chr15:77711899-77711949	NB4	blood:	n/a
25	chr15:77711899-77711949	Hepatocyte	liver:	n/a
26	chr15:77711899-77711949	CMK	blood:	n/a
27	chr15:77711899-77711949	HNPCEpiC	eye:	n/a
28	chr15:77711899-77711949	GM12878	blood:	n/a
29	chr15:77711899-77711949	HEEpiC	esophagus:	n/a
30	chr15:77711899-77711949	A549	lung:	n/a
31	chr15:77711899-77711949	GM19239	blood:	n/a
32	chr15:77711899-77711949	HRCEpiC	kidney:	n/a
33	chr15:77711899-77711949	AG04449	skin:	fetal
34	chr15:77711899-77711949	HMEC	breast:	n/a
35	chr15:77711899-77711949	T-47D	breast:	n/a
36	chr15:77711899-77711949	NHBE	bronchial:	n/a
37	chr15:77711899-77711949	IMR90	lung:	fetal
38	chr15:77711899-77711949	GM12891	blood:	n/a
39	chr15:77711899-77711949	Jurkat	blood:	n/a
40	chr15:77711899-77711949	HRE	kidney:	n/a
41	chr15:77711899-77711949	Hela-S3	cervix:	n/a
42	chr15:77711899-77711949	HCPEpiC	choroid plexus:	n/a
43	chr15:77711899-77711949	LNCaP	prostate:	n/a
44	chr15:77711899-77711949	PFSK-1	brain:	n/a
45	chr15:77711899-77711949	RPTEC	kidney:	n/a
46	chr15:77711899-77711949	MCF10A-Er-Src	breast:	n/a
47	chr15:77711899-77711949	NH-A	brain:	n/a
48	chr15:77711899-77711949	U87	brain:	n/a
49	chr15:77711899-77711949	MCF-7	breast:	n/a
50	chr15:77711899-77711949	NHDF-neo	bronchial:	n/a

Variant related genes	Relation type
HMG20A	TF binding region
HMG20A	CpG island

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	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv482689	chr15:77576396-77731559	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv21291	chr15:77707945-77712363	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3422226	chr15:77710922-77713870	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
8	esv3327387	chr15:77711172-77713620	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
9	esv3373572	chr15:77711697-77713495	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77709600-77712600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:77709600-77713800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr15:77710200-77713600	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr15:77710200-77714400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:77710200-77714400	Active TSS	Right Atrium	heart
6	chr15:77710400-77713800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:77710400-77714400	Active TSS	Right Ventricle	heart
8	chr15:77710400-77714400	Active TSS	NHDF-Ad	bronchial
9	chr15:77710400-77714600	Active TSS	NHLF	lung
10	chr15:77710600-77713600	Active TSS	HSMMtube	muscle
11	chr15:77710600-77713800	Active TSS	Colon Smooth Muscle	Colon
12	chr15:77710600-77713800	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr15:77710600-77714200	Active TSS	H1 Cell Line	embryonic stem cell
14	chr15:77710600-77714200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:77710600-77714600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:77710800-77712000	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr15:77710800-77712000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:77710800-77713600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:77710800-77713600	Active TSS	Fetal Kidney	kidney
20	chr15:77710800-77713600	Active TSS	Placenta	Placenta
21	chr15:77710800-77713800	Active TSS	Duodenum Mucosa	Duodenum
22	chr15:77710800-77714000	Active TSS	Colonic Mucosa	Colon
23	chr15:77710800-77714000	Active TSS	Left Ventricle	heart
24	chr15:77710800-77714200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:77710800-77714200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:77710800-77714200	Active TSS	Fetal Muscle Trunk	muscle
27	chr15:77710800-77714200	Active TSS	Psoas Muscle	Psoas
28	chr15:77710800-77714600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr15:77711000-77712000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:77711000-77713600	Active TSS	Fetal Muscle Leg	muscle
31	chr15:77711000-77713800	Active TSS	Fetal Stomach	stomach
32	chr15:77711000-77713800	Active TSS	Osteobl	bone
33	chr15:77711000-77714000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr15:77711000-77714000	Active TSS	Lung	lung
35	chr15:77711000-77714000	Active TSS	Ovary	ovary
36	chr15:77711000-77714000	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr15:77711000-77714200	Active TSS	Aorta	Aorta
38	chr15:77711000-77714400	Active TSS	Stomach Smooth Muscle	stomach
39	chr15:77711000-77714800	Active TSS	K562	blood
40	chr15:77711200-77712000	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr15:77711200-77712000	Active TSS	Fetal Heart	heart
42	chr15:77711200-77713400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr15:77711200-77713600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:77711200-77713600	Active TSS	Brain Substantia Nigra	brain
45	chr15:77711200-77713600	Active TSS	Fetal Lung	lung
46	chr15:77711200-77713600	Active TSS	HUVEC	blood vessel
47	chr15:77711200-77713600	Active TSS	NH-A	brain
48	chr15:77711200-77713800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:77711200-77713800	Active TSS	Brain Angular Gyrus	brain
50	chr15:77711200-77713800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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