Variant report

Variant	rs563353378
Chromosome Location	chr16:30545541-30545542
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:86)
CpG islands
(count:61)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:86 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:30545378-30547485	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr16:30545526-30547407	GM19099	blood:	n/a	n/a
3	POLR2A	chr16:30545269-30546761	MCF-7	breast:	n/a	n/a
4	TAF1	chr16:30545323-30546591	HepG2	liver:	n/a	n/a
5	POLR2A	chr16:30545471-30546702	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr16:30537047-30547480	HepG2	liver:	n/a	n/a
7	POLR2A	chr16:30545237-30546243	GM12891	blood:	n/a	n/a
8	POLR2A	chr16:30545516-30547300	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr16:30545377-30547476	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr16:30545540-30547380	MCF10A-Er-Src	breast:	n/a	n/a
11	TAF1	chr16:30545324-30547329	H1-hESC	embryonic stem cell:	n/a	n/a
12	EBF1	chr16:30545291-30545822	GM12878	blood:	n/a	chr16:30545486-30545497 chr16:30545486-30545499
13	ZEB1	chr16:30545475-30546598	GM12878	blood:	n/a	chr16:30546350-30546357 chr16:30545510-30545523
14	POLR2A	chr16:30545082-30547574	K562	blood:	n/a	n/a
15	MAX	chr16:30545502-30547441	A549	lung:	n/a	chr16:30547147-30547157 chr16:30547382-30547390
16	POLR2A	chr16:30545506-30546710	GM18951	blood:	n/a	n/a
17	POLR2A	chr16:30545479-30547554	K562	blood:	n/a	n/a
18	MAX	chr16:30545459-30547593	HepG2	liver:	n/a	chr16:30547147-30547157 chr16:30547382-30547390
19	YY1	chr16:30544983-30546673	GM12892	blood:	n/a	chr16:30546286-30546294 chr16:30546287-30546297 chr16:30546173-30546185 chr16:30546275-30546297 chr16:30546280-30546299
20	POLR2A	chr16:30545494-30546929	ECC-1	luminal epithelium:	n/a	n/a
21	HCFC1	chr16:30544857-30547593	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr16:30545073-30547561	GM12892	blood:	n/a	n/a
23	POLR2A	chr16:30545038-30547584	HepG2	liver:	n/a	n/a
24	POLR2A	chr16:30545534-30545550	H1-hESC	embryonic stem cell:	n/a	n/a
25	RUNX3	chr16:30545486-30547442	GM12878	blood:	n/a	n/a
26	POLR2A	chr16:30545234-30547618	GM12891	blood:	n/a	n/a
27	POLR2A	chr16:30544440-30547500	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr16:30545070-30548080	GM12878	blood:	n/a	n/a
29	TAF1	chr16:30545525-30546927	GM12878	blood:	n/a	n/a
30	CBX3	chr16:30545392-30547589	K562	blood:	n/a	n/a
31	POLR2A	chr16:30545509-30547459	Hela-S3	cervix:	n/a	n/a
32	MXI1	chr16:30545441-30547622	SK-N-SH	brain:	n/a	chr16:30547380-30547389
33	PML	chr16:30545490-30547702	GM12878	blood:	n/a	n/a
34	POLR2A	chr16:30545519-30546802	GM18526	blood:	n/a	n/a
35	NFIC	chr16:30545478-30547592	GM12878	blood:	n/a	n/a
36	TAF1	chr16:30545268-30546521	HepG2	liver:	n/a	n/a
37	HEY1	chr16:30545095-30547507	HepG2	liver:	n/a	chr16:30546243-30546258
38	RAD21	chr16:30545518-30546550	H1-hESC	embryonic stem cell:	n/a	chr16:30546105-30546117 chr16:30546103-30546110 chr16:30546248-30546262
39	POLR2A	chr16:30545207-30547624	GM12891	blood:	n/a	n/a
40	TCF12	chr16:30545393-30546993	A549	lung:	n/a	n/a
41	MAX	chr16:30545456-30547508	HepG2	liver:	n/a	chr16:30547147-30547157 chr16:30547382-30547390
42	POLR2A	chr16:30545530-30546803	PFSK-1	brain:	n/a	n/a
43	ELF1	chr16:30545379-30546817	GM12878	blood:	n/a	chr16:30546180-30546189
44	POLR2A	chr16:30545361-30547446	Hela-S3	cervix:	n/a	n/a
45	THAP1	chr16:30545517-30546649	K562	blood:	n/a	chr16:30546272-30546296
46	POLR2A	chr16:30545164-30547384	GM12892	blood:	n/a	n/a
47	MTA3	chr16:30545047-30547791	GM12878	blood:	n/a	n/a
48	POLR2A	chr16:30545534-30546579	Gliobla	brain:	n/a	n/a
49	POLR2A	chr16:30545514-30547398	PBDE	blood:	n/a	n/a
50	POLR2A	chr16:30545412-30546639	A549	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr16:30545507-30545557	AG09319	gingival:	n/a
2	chr16:30545507-30545557	T-47D	breast:	n/a
3	chr16:30545507-30545557	MCF10A-Er-Src	breast:	n/a
4	chr16:30545507-30545557	HPAEpiC	pulmonary alveolar:	n/a
5	chr16:30545507-30545557	GM19239	blood:	n/a
6	chr16:30545507-30545557	Jurkat	blood:	n/a
7	chr16:30545507-30545557	NB4	blood:	n/a
8	chr16:30545507-30545557	AG04450	lung:	fetal
9	chr16:30545507-30545557	SKMC	muscle:	n/a
10	chr16:30545507-30545557	SK-N-SH	brain:	n/a
11	chr16:30545507-30545557	MCF-7	breast:	n/a
12	chr16:30545507-30545557	SK-N-MC	brain:	n/a
13	chr16:30545507-30545557	SK-N-SH_RA	brain:	n/a
14	chr16:30545507-30545557	HL-60	blood:	n/a
15	chr16:30545507-30545557	HAEpiC	amniotic membrane:	n/a
16	chr16:30545507-30545557	HRCEpiC	kidney:	n/a
17	chr16:30545507-30545557	AG04449	skin:	fetal
18	chr16:30545507-30545557	GM12891	blood:	n/a
19	chr16:30545507-30545557	IMR90	lung:	fetal
20	chr16:30545507-30545557	LNCaP	prostate:	n/a
21	chr16:30545507-30545557	GM12878	blood:	n/a
22	chr16:30545507-30545557	PrEC	prostate:	n/a
23	chr16:30545507-30545557	Caco-2	colon:	n/a
24	chr16:30545507-30545557	BJ	skin:	n/a
25	chr16:30545507-30545557	NT2-D1	testis:	n/a
26	chr16:30545507-30545557	ovcar-3	ovarian:	n/a
27	chr16:30545507-30545557	CMK	blood:	n/a
28	chr16:30545507-30545557	HMEC	breast:	n/a
29	chr16:30545507-30545557	PANC-1	pancreas:	n/a
30	chr16:30545507-30545557	NHDF-neo	bronchial:	n/a
31	chr16:30545507-30545557	HRPEpiC	eye:	n/a
32	chr16:30545507-30545557	A549	lung:	n/a
33	chr16:30545507-30545557	NH-A	brain:	n/a
34	chr16:30545507-30545557	HepG2	liver:	n/a
35	chr16:30545507-30545557	AG09309	skin:	n/a
36	chr16:30545507-30545557	ProgFib	skin:	n/a
37	chr16:30545507-30545557	HRE	kidney:	n/a
38	chr16:30545507-30545557	BE2_C	brain:	n/a
39	chr16:30545507-30545557	Hepatocyte	liver:	n/a
40	chr16:30545507-30545557	HCF	heart:	n/a
41	chr16:30545507-30545557	SAEC	small airway:	n/a
42	chr16:30545507-30545557	HCT-116	colon:	n/a
43	chr16:30545507-30545557	HUVEC	blood vessel:	n/a
44	chr16:30545507-30545557	HIPEpiC	eye:	n/a
45	chr16:30545507-30545557	HCM	heart:	n/a
46	chr16:30545507-30545557	AoSMC	blood vessel:	n/a
47	chr16:30545507-30545557	GM06990	blood:	n/a
48	chr16:30545507-30545557	H1-hESC	embryonic stem cell:	embryo
49	chr16:30545507-30545557	Hela-S3	cervix:	n/a
50	chr16:30545507-30545557	RPTEC	kidney:	n/a

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30545157..30547413-chr16:30708234..30710909,2	K562	blood:
2	chr16:30439809..30443048-chr16:30544747..30548003,3	K562	blood:
3	chr16:30545060..30546594-chr16:30668041..30670734,2	K562	blood:
4	chr16:30074349..30076669-chr16:30543330..30545893,2	MCF-7	breast:
5	chr16:30541129..30548783-chr16:30576543..30583587,16	MCF-7	breast:
6	chr16:30544664..30548849-chr16:30597277..30601099,4	K562	blood:
7	chr16:30544644..30549200-chr16:30579756..30585399,7	K562	blood:
8	chr16:30544819..30547359-chr16:30669370..30671346,2	MCF-7	breast:
9	chr16:30534557..30548684-chr16:30561877..30572653,49	MCF-7	breast:
10	chr16:30544371..30547496-chr16:30661598..30664666,3	K562	blood:
11	chr16:30544993..30547961-chr16:30709430..30711142,2	MCF-7	breast:
12	chr16:30454223..30458795-chr16:30544992..30549263,8	K562	blood:
13	chr16:30545394..30548849-chr16:30597035..30599710,5	K562	blood:
14	chr16:30440428..30442526-chr16:30544936..30546517,2	K562	blood:
15	chr1:149857820..149858393-chr16:30545109..30545891,2	Hela-S3	cervix:
16	chr16:30543696..30550338-chr16:30595198..30599305,8	MCF-7	breast:
17	chr16:30440316..30443197-chr16:30545164..30548518,4	MCF-7	breast:
18	chr16:30454856..30459511-chr16:30543910..30548861,10	K562	blood:
19	chr16:30439652..30442096-chr16:30544594..30547144,2	MCF-7	breast:
20	chr16:30541481..30548892-chr16:30595486..30600580,13	MCF-7	breast:
21	chr16:30545465..30548885-chr16:30620195..30623109,3	MCF-7	breast:
22	chr16:30453263..30460635-chr16:30534974..30549190,40	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000235560	TF binding region
ENSG00000235560	CpG island
ENSG00000229809	Chromatin interaction
ENSG00000260869	Chromatin interaction
ENSG00000261840	Chromatin interaction
ENSG00000156858	Chromatin interaction
ENSG00000156853	Chromatin interaction
ENSG00000179958	Chromatin interaction
ENSG00000149925	Chromatin interaction
ENSG00000261588	Chromatin interaction
ENSG00000179918	Chromatin interaction
ENSG00000169951	Chromatin interaction
ENSG00000156860	Chromatin interaction
ENSG00000239791	Chromatin interaction
ENSG00000197162	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000080603	Chromatin interaction
ENSG00000260167	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
2	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
4	nsv905726	chr16:30528272-30546488	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Enhancers 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	50 gene(s)	inside rSNPs	diseases
5	esv3390311	chr16:30544451-30567432	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 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	chr16:30544400-30545600	Flanking Active TSS	Liver	Liver
2	chr16:30544400-30546200	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr16:30544600-30545600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr16:30544600-30545600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
5	chr16:30544600-30545800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr16:30544600-30546400	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr16:30544600-30546400	Active TSS	Osteobl	bone
8	chr16:30544600-30547200	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr16:30544600-30547200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr16:30544600-30547600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr16:30544800-30545600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr16:30544800-30546600	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr16:30544800-30546800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr16:30544800-30547400	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr16:30544800-30547400	Active TSS	Gastric	stomach
16	chr16:30544800-30547600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr16:30544800-30547600	Active TSS	Fetal Kidney	kidney
18	chr16:30544800-30547800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr16:30544800-30547800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr16:30545000-30545600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr16:30545000-30545600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr16:30545000-30545600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr16:30545000-30545600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr16:30545000-30545600	Flanking Active TSS	Fetal Lung	lung
25	chr16:30545000-30545600	Flanking Active TSS	Fetal Muscle Trunk	muscle
26	chr16:30545000-30545600	Flanking Active TSS	Fetal Muscle Leg	muscle
27	chr16:30545000-30545800	Flanking Active TSS	Primary B cells from peripheral blood	blood
28	chr16:30545000-30545800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr16:30545000-30546000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr16:30545000-30546000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr16:30545000-30546000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr16:30545000-30546200	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr16:30545000-30546200	Flanking Active TSS	HMEC	breast
34	chr16:30545000-30546600	Bivalent/Poised TSS	HepG2	liver
35	chr16:30545000-30546800	Active TSS	Duodenum Mucosa	Duodenum
36	chr16:30545000-30547200	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr16:30545000-30547200	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr16:30545000-30547200	Active TSS	Pancreas	Pancrea
39	chr16:30545000-30547200	Active TSS	GM12878-XiMat	blood
40	chr16:30545000-30547200	Active TSS	Hela-S3	cervix
41	chr16:30545000-30547400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr16:30545200-30545600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr16:30545200-30545600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr16:30545200-30545600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr16:30545200-30545600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr16:30545200-30545600	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr16:30545200-30545600	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr16:30545200-30545600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr16:30545200-30545600	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr16:30545200-30545600	Flanking Active TSS	Fetal Thymus	thymus

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