Variant report

Variant	rs544621524
Chromosome Location	chr1:85462862-85462863
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	ZEB1	chr1:85462507-85463768	GM12878	blood:	n/a	n/a
2	EBF1	chr1:85461040-85464248	GM12878	blood:	n/a	chr1:85463075-85463084 chr1:85462912-85462922 chr1:85463073-85463084
3	USF2	chr1:85462149-85462959	GM12878	blood:	n/a	n/a
4	SIN3AK20	chr1:85462371-85463242	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr1:85459671-85465061	GM12892	blood:	n/a	n/a
6	TBP	chr1:85461053-85462869	GM12878	blood:	n/a	n/a
7	CTCF	chr1:85462780-85462930	HPF	lung:	n/a	n/a
8	E2F6	chr1:85462424-85463020	H1-hESC	embryonic stem cell:	n/a	chr1:85462835-85462844 chr1:85462827-85462839 chr1:85462983-85462992
9	MYC	chr1:85462642-85462929	MCF-7	breast:	n/a	chr1:85462813-85462822
10	EGR1	chr1:85462855-85463145	GM12878	blood:	n/a	chr1:85462978-85462991 chr1:85462979-85462993 chr1:85462950-85462960
11	POLR2A	chr1:85461049-85464327	GM18951	blood:	n/a	n/a
12	MAX	chr1:85462304-85463390	H1-hESC	embryonic stem cell:	n/a	chr1:85462813-85462822 chr1:85463085-85463094
13	POLR2A	chr1:85461494-85464994	GM12892	blood:	n/a	n/a
14	MAX	chr1:85462145-85463701	GM12878	blood:	n/a	chr1:85462813-85462822 chr1:85463085-85463094
15	CTCF	chr1:85462820-85462970	GM12864	blood:	n/a	n/a
16	ZNF143	chr1:85462642-85463259	GM12878	blood:	n/a	chr1:85463074-85463092 chr1:85463202-85463220 chr1:85462987-85463005
17	POLR2A	chr1:85461102-85464291	GM18526	blood:	n/a	n/a
18	ELF1	chr1:85462435-85463628	GM12878	blood:	n/a	chr1:85462980-85462989
19	ZBTB7A	chr1:85462564-85463389	ECC-1	luminal epithelium:	n/a	chr1:85463071-85463079
20	MTA3	chr1:85460680-85464125	GM12878	blood:	n/a	n/a
21	USF1	chr1:85462253-85462969	H1-hESC	embryonic stem cell:	n/a	n/a
22	TCF3	chr1:85462514-85462948	GM12878	blood:	n/a	n/a
23	STAT5A	chr1:85460893-85463850	GM12878	blood:	n/a	chr1:85463447-85463455 chr1:85461389-85461400
24	POLR2A	chr1:85459807-85464317	GM12892	blood:	n/a	n/a
25	CTCF	chr1:85462760-85462910	HCPEpiC	choroid plexus:	n/a	n/a
26	POLR2A	chr1:85462413-85463573	GM12878	blood:	n/a	n/a
27	RELA	chr1:85461141-85463082	GM12892	blood:	n/a	n/a
28	BACH1	chr1:85462556-85462963	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr1:85462319-85463395	A549	lung:	n/a	chr1:85462813-85462822 chr1:85463085-85463094
30	MAX	chr1:85462559-85463420	MCF-7	breast:	n/a	chr1:85462813-85462822 chr1:85463085-85463094
31	CTCF	chr1:85462780-85462930	AG09319	gingival:	n/a	n/a
32	PAX5	chr1:85462571-85463524	GM12892	blood:	n/a	n/a
33	POLR2A	chr1:85461608-85463709	GM15510	blood:	n/a	n/a
34	RELA	chr1:85461055-85463441	GM15510	blood:	n/a	n/a
35	CTCF	chr1:85462820-85462970	HMEC	breast:	n/a	n/a
36	CTCF	chr1:85462840-85462990	GM12865	blood:	n/a	n/a
37	POLR2A	chr1:85462419-85462989	SK-N-MC	brain:	n/a	n/a
38	POLR2A	chr1:85459795-85464999	GM12878	blood:	n/a	n/a
39	RELA	chr1:85461051-85463198	GM19099	blood:	n/a	n/a
40	CTCF	chr1:85462860-85463010	AoAF	blood vessel:	n/a	n/a
41	POLR2A	chr1:85462437-85463237	GM10847	blood:	n/a	n/a
42	PAX5	chr1:85462466-85463133	GM12878	blood:	n/a	n/a
43	TAF1	chr1:85462449-85462962	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr1:85460981-85465011	GM19099	blood:	n/a	n/a
45	CTCF	chr1:85462760-85462910	GM12868	blood:	n/a	n/a
46	CHD2	chr1:85461067-85464026	GM12878	blood:	n/a	chr1:85462833-85462843 chr1:85462244-85462251
47	PAX5	chr1:85462852-85463026	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:85461031-85464258	GM12892	blood:	n/a	n/a
49	CTCF	chr1:85462742-85463425	GM12878	blood:	n/a	n/a
50	POLR2A	chr1:85461655-85462966	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:85462857-85462907	Caco-2	colon:	n/a
2	chr1:85462857-85462907	HPAEpiC	pulmonary alveolar:	n/a
3	chr1:85462812-85462862	HRPEpiC	eye:	n/a
4	chr1:85462857-85462907	SAEC	small airway:	n/a
5	chr1:85462857-85462907	T-47D	breast:	n/a
6	chr1:85462857-85462907	HEEpiC	esophagus:	n/a
7	chr1:85462812-85462862	HEK293	kidney:	embryo
8	chr1:85462857-85462907	ovcar-3	ovarian:	n/a
9	chr1:85462812-85462862	HCT-116	colon:	n/a
10	chr1:85462857-85462907	HRCEpiC	kidney:	n/a
11	chr1:85462857-85462907	NHBE	bronchial:	n/a
12	chr1:85462812-85462862	HPAEpiC	pulmonary alveolar:	n/a
13	chr1:85462812-85462862	AoSMC	blood vessel:	n/a
14	chr1:85462812-85462862	RPTEC	kidney:	n/a
15	chr1:85462812-85462862	HCF	heart:	n/a
16	chr1:85462812-85462862	MCF10A-Er-Src	breast:	n/a
17	chr1:85462812-85462862	T-47D	breast:	n/a
18	chr1:85462857-85462907	NH-A	brain:	n/a
19	chr1:85462812-85462862	NHBE	bronchial:	n/a
20	chr1:85462812-85462862	GM12878	blood:	n/a
21	chr1:85462812-85462862	SK-N-MC	brain:	n/a
22	chr1:85462812-85462862	HUVEC	blood vessel:	n/a
23	chr1:85462857-85462907	AoSMC	blood vessel:	n/a
24	chr1:85462857-85462907	PrEC	prostate:	n/a
25	chr1:85462812-85462862	ovcar-3	ovarian:	n/a
26	chr1:85462857-85462907	BE2_C	brain:	n/a
27	chr1:85462812-85462862	BJ	skin:	n/a
28	chr1:85462812-85462862	AG04449	skin:	fetal
29	chr1:85462812-85462862	LNCaP	prostate:	n/a
30	chr1:85462857-85462907	HRE	kidney:	n/a
31	chr1:85462857-85462907	BJ	skin:	n/a
32	chr1:85462857-85462907	ProgFib	skin:	n/a
33	chr1:85462857-85462907	GM19239	blood:	n/a
34	chr1:85462812-85462862	HL-60	blood:	n/a
35	chr1:85462857-85462907	HCM	heart:	n/a
36	chr1:85462857-85462907	NT2-D1	testis:	n/a
37	chr1:85462857-85462907	HepG2	liver:	n/a
38	chr1:85462857-85462907	GM06990	blood:	n/a
39	chr1:85462812-85462862	AG09319	gingival:	n/a
40	chr1:85462857-85462907	SKMC	muscle:	n/a
41	chr1:85462857-85462907	AG04449	skin:	fetal
42	chr1:85462812-85462862	AG10803	skin:	n/a
43	chr1:85462812-85462862	Jurkat	blood:	n/a
44	chr1:85462812-85462862	ECC-1	luminal epithelium:	n/a
45	chr1:85462857-85462907	HCT-116	colon:	n/a
46	chr1:85462857-85462907	Hela-S3	cervix:	n/a
47	chr1:85462812-85462862	Caco-2	colon:	n/a
48	chr1:85462812-85462862	SAEC	small airway:	n/a
49	chr1:85462812-85462862	BE2_C	brain:	n/a
50	chr1:85462812-85462862	U87	brain:	n/a

Variant related genes	Relation type
WDR63	TF binding region
MCOLN2	TF binding region
MCOLN2	CpG island
WDR63	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	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	esv3515392	chr1:85437980-85465392	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3515393	chr1:85437980-85465392	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
9	esv3410983	chr1:85461789-85464337	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85460400-85463800	Active TSS	GM12878-XiMat	blood
2	chr1:85461200-85463400	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr1:85461600-85464400	Active TSS	Primary T helper naive cells from peripheral blood	blood
4	chr1:85461800-85463200	Active TSS	Rectal Smooth Muscle	rectum
5	chr1:85461800-85463200	Active TSS	A549	lung
6	chr1:85461800-85463600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:85461800-85464400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr1:85461800-85464600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr1:85462000-85463000	Active TSS	Colonic Mucosa	Colon
10	chr1:85462000-85463000	Active TSS	Right Ventricle	heart
11	chr1:85462000-85464200	Bivalent/Poised TSS	Brain Substantia Nigra	brain
12	chr1:85462000-85464400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr1:85462000-85464400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
14	chr1:85462000-85464600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
15	chr1:85462200-85463000	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:85462200-85463000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:85462200-85463000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:85462200-85463000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:85462200-85463000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:85462200-85463000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:85462200-85463000	Active TSS	Lung	lung
22	chr1:85462200-85463000	Active TSS	Ovary	ovary
23	chr1:85462200-85463000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
24	chr1:85462200-85463000	Active TSS	HMEC	breast
25	chr1:85462200-85463200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:85462200-85463200	Bivalent/Poised TSS	NH-A	brain
27	chr1:85462200-85463400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:85462200-85463400	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr1:85462200-85463600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
30	chr1:85462200-85463600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
31	chr1:85462200-85464000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:85462200-85464200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr1:85462200-85464200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:85462200-85464200	Active TSS	Aorta	Aorta
35	chr1:85462400-85463000	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:85462400-85463000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:85462400-85463200	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:85462400-85463200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:85462400-85463200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:85462400-85463200	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr1:85462400-85463200	Active TSS	Brain Hippocampus Middle	brain
42	chr1:85462400-85463200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
43	chr1:85462400-85463200	Active TSS	Gastric	stomach
44	chr1:85462400-85463200	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr1:85462400-85463200	Bivalent/Poised TSS	HSMMtube	muscle
46	chr1:85462400-85463400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:85462400-85463400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:85462400-85463400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
49	chr1:85462400-85463600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:85462400-85463600	Active TSS	NHDF-Ad	bronchial

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