Variant report

Variant	rs543041666
Chromosome Location	chr1:47903267-47903268
allele	A/C
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	SP1	chr1:47903244-47903747	A549	lung:	n/a	chr1:47903692-47903701 chr1:47903391-47903400 chr1:47903692-47903706 chr1:47903697-47903709 chr1:47903392-47903401 chr1:47903385-47903397 chr1:47903385-47903397 chr1:47903697-47903709 chr1:47903391-47903400 chr1:47903693-47903702 chr1:47903691-47903703 chr1:47903386-47903395 chr1:47903699-47903708 chr1:47903691-47903703 chr1:47903692-47903702
2	POLR2A	chr1:47902127-47903588	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:47902800-47903644	GM12878	blood:	n/a	n/a
4	CTCF	chr1:47901969-47903966	A549	lung:	n/a	chr1:47903695-47903708 chr1:47903638-47903654 chr1:47903640-47903649 chr1:47903639-47903660 chr1:47903640-47903653 chr1:47903637-47903655 chr1:47903640-47903653 chr1:47903642-47903652 chr1:47902578-47902591
5	SIN3A	chr1:47902874-47903634	GM12878	blood:	n/a	chr1:47902880-47902893 chr1:47902881-47902892
6	POLR2A	chr1:47903009-47903885	MCF-7	breast:	n/a	n/a
7	CTCF	chr1:47902083-47903846	IMR90	lung:	n/a	chr1:47903695-47903708 chr1:47903638-47903654 chr1:47903640-47903649 chr1:47903639-47903660 chr1:47903640-47903653 chr1:47903637-47903655 chr1:47903640-47903653 chr1:47903642-47903652 chr1:47902578-47902591
8	ZBTB7A	chr1:47903195-47904200	ECC-1	luminal epithelium:	n/a	chr1:47903645-47903654
9	YY1	chr1:47903176-47903428	HCT-116	colon:	n/a	chr1:47903322-47903331
10	HEY1	chr1:47903011-47903970	K562	blood:	n/a	chr1:47903782-47903797 chr1:47903546-47903561 chr1:47903130-47903145 chr1:47903317-47903332 chr1:47903405-47903420 chr1:47903760-47903775 chr1:47903646-47903661
11	TCF7L2	chr1:47902190-47903850	HCT-116	colon:	n/a	n/a
12	ELF1	chr1:47902073-47903938	K562	blood:	n/a	chr1:47903423-47903436 chr1:47903588-47903600 chr1:47903133-47903145 chr1:47903288-47903300 chr1:47903322-47903331 chr1:47903787-47903796 chr1:47903785-47903797 chr1:47903292-47903301 chr1:47903793-47903802 chr1:47903655-47903667 chr1:47903784-47903793 chr1:47903788-47903800 chr1:47903315-47903327
13	RCOR1	chr1:47901790-47903838	K562	blood:	n/a	n/a
14	POLR2A	chr1:47902754-47903955	K562	blood:	n/a	n/a
15	CTCF	chr1:47903212-47903816	H1-hESC	embryonic stem cell:	n/a	chr1:47903695-47903708 chr1:47903638-47903654 chr1:47903640-47903649 chr1:47903639-47903660 chr1:47903640-47903653 chr1:47903637-47903655 chr1:47903640-47903653 chr1:47903642-47903652
16	UBTF	chr1:47902126-47904027	K562	blood:	n/a	n/a
17	ZBTB7A	chr1:47902143-47904182	K562	blood:	n/a	chr1:47903645-47903654
18	TBP	chr1:47903047-47903955	K562	blood:	n/a	n/a
19	EGR1	chr1:47903043-47904080	HCT-116	colon:	n/a	chr1:47903693-47903708 chr1:47903694-47903707 chr1:47903657-47903667 chr1:47903691-47903705 chr1:47903692-47903702 chr1:47903695-47903705 chr1:47903694-47903707
20	NR2F2	chr1:47903080-47903844	K562	blood:	n/a	n/a
21	MAX	chr1:47902072-47903880	NB4	blood:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
22	POLR2A	chr1:47903090-47903692	GM10847	blood:	n/a	n/a
23	POLR2A	chr1:47902034-47904062	HEK293	kidney:	n/a	n/a
24	POLR2A	chr1:47903125-47903591	A549	lung:	n/a	n/a
25	POLR2A	chr1:47902966-47903703	HUVEC	blood vessel:	n/a	n/a
26	BCLAF1	chr1:47903237-47903713	GM12878	blood:	n/a	chr1:47903239-47903252 chr1:47903318-47903327 chr1:47903323-47903332 chr1:47903319-47903332 chr1:47903320-47903329 chr1:47903312-47903325 chr1:47903692-47903701 chr1:47903589-47903602 chr1:47903587-47903600 chr1:47903546-47903559
27	POLR2A	chr1:47902903-47904044	MCF-7	breast:	n/a	n/a
28	ELF1	chr1:47903113-47903826	MCF-7	breast:	n/a	chr1:47903423-47903436 chr1:47903588-47903600 chr1:47903133-47903145 chr1:47903288-47903300 chr1:47903322-47903331 chr1:47903787-47903796 chr1:47903785-47903797 chr1:47903292-47903301 chr1:47903793-47903802 chr1:47903655-47903667 chr1:47903784-47903793 chr1:47903788-47903800 chr1:47903315-47903327
29	CREB1	chr1:47903133-47904066	GM12878	blood:	n/a	n/a
30	ZNF143	chr1:47903163-47903852	K562	blood:	n/a	chr1:47903172-47903190 chr1:47903646-47903656 chr1:47903695-47903713 chr1:47903388-47903406 chr1:47903311-47903321
31	SIN3A	chr1:47902890-47903810	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr1:47903099-47903901	HCT-116	colon:	n/a	chr1:47903695-47903708 chr1:47903638-47903654 chr1:47903640-47903649 chr1:47903639-47903660 chr1:47903640-47903653 chr1:47903637-47903655 chr1:47903640-47903653 chr1:47903642-47903652
33	POLR2A	chr1:47903052-47903937	Hela-S3	cervix:	n/a	n/a
34	CHD2	chr1:47903100-47903735	K562	blood:	n/a	chr1:47903702-47903712 chr1:47903380-47903390
35	EGR1	chr1:47903214-47903872	K562	blood:	n/a	chr1:47903693-47903708 chr1:47903694-47903707 chr1:47903657-47903667 chr1:47903691-47903705 chr1:47903692-47903702 chr1:47903695-47903705 chr1:47903694-47903707
36	CHD1	chr1:47902881-47903637	GM12878	blood:	n/a	chr1:47903380-47903390
37	ZBTB7A	chr1:47903175-47904259	ECC-1	luminal epithelium:	n/a	chr1:47903645-47903654
38	POLR2A	chr1:47902066-47903914	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr1:47903110-47903899	PFSK-1	brain:	n/a	n/a
40	HEY1	chr1:47903181-47903426	HepG2	liver:	n/a	chr1:47903317-47903332 chr1:47903405-47903420
41	MAX	chr1:47902080-47904090	HepG2	liver:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
42	CREB1	chr1:47902014-47904068	HepG2	liver:	n/a	n/a
43	ELF1	chr1:47902991-47903831	K562	blood:	n/a	chr1:47903423-47903436 chr1:47903588-47903600 chr1:47903133-47903145 chr1:47903288-47903300 chr1:47903322-47903331 chr1:47903787-47903796 chr1:47903785-47903797 chr1:47903292-47903301 chr1:47903793-47903802 chr1:47903655-47903667 chr1:47903784-47903793 chr1:47903788-47903800 chr1:47903315-47903327
44	BACH1	chr1:47903013-47903914	H1-hESC	embryonic stem cell:	n/a	n/a
45	CCNT2	chr1:47902133-47904058	K562	blood:	n/a	chr1:47903693-47903702
46	POLR2A	chr1:47902971-47903893	PANC-1	pancreas:	n/a	n/a
47	EP300	chr1:47903065-47904014	ECC-1	luminal epithelium:	n/a	chr1:47903588-47903597 chr1:47903639-47903655 chr1:47903786-47903795 chr1:47903789-47903798 chr1:47903591-47903600
48	MAZ	chr1:47901897-47903976	GM12878	blood:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
49	RELA	chr1:47903025-47903687	GM15510	blood:	n/a	n/a
50	CTCF	chr1:47903025-47903779	Spleen_OC	spleen:	n/a	chr1:47903695-47903708 chr1:47903638-47903654 chr1:47903640-47903649 chr1:47903639-47903660 chr1:47903640-47903653 chr1:47903637-47903655 chr1:47903640-47903653 chr1:47903642-47903652

No.	Distal block	Cell Line	Cell type
1	chr1:47901774..47903783-chr1:47905502..47907193,2	MCF-7	breast:
2	chr1:47901790..47903824-chr1:48190200..48191775,2	K562	blood:
3	chr1:47894501..47897089-chr1:47902727..47904976,2	MCF-7	breast:
4	chr1:47903242..47903875-chr1:48191604..48192572,3	K562	blood:
5	chr1:47902221..47904815-chr1:47929260..47931018,2	K562	blood:
6	chr1:8938373..8938983-chr1:47903127..47904074,2	HCT-116	colon:
7	chr1:47902455..47903363-chr10:89577216..89577997,2	Hela-S3	cervix:
8	chr1:47901999..47903599-chr1:48174794..48176429,2	MCF-7	breast:
9	chr1:47903024..47904874-chr1:47914470..47916409,2	K562	blood:
10	chr1:47902477..47903371-chr9:131218074..131218707,2	Hela-S3	cervix:
11	chr1:47902934..47903670-chr1:47913431..47914329,2	K562	blood:
12	chr1:47902862..47904142-chr1:48175786..48176848,4	K562	blood:

Variant related genes	Relation type
FOXD2-AS1	TF binding region
ENSG00000074800	Chromatin interaction
ENSG00000138138	Chromatin interaction
ENSG00000136811	Chromatin interaction
ENSG00000223820	Chromatin interaction
ENSG00000230679	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	nsv871961	chr1:47875627-47912628	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534956	chr1:47882277-47905486	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv534957	chr1:47882277-47907965	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1001779	chr1:47884229-48111485	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv871299	chr1:47889417-48057890	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv3432093	chr1:47901465-47906063	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	esv3406880	chr1:47901890-47905238	Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47899000-47904400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:47901400-47908000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
3	chr1:47901800-47904000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
4	chr1:47901800-47904600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:47902000-47903600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:47902000-47904400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
7	chr1:47902000-47904400	Active TSS	A549	lung
8	chr1:47902000-47904800	Active TSS	Sigmoid Colon	Sigmoid Colon
9	chr1:47902200-47903600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr1:47902200-47904000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:47902200-47904000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:47902200-47904000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
13	chr1:47902200-47904000	Active TSS	Hela-S3	cervix
14	chr1:47902200-47904200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:47902200-47904200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:47902200-47904200	Active TSS	HMEC	breast
17	chr1:47902200-47904200	Active TSS	K562	blood
18	chr1:47902200-47904400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:47902200-47904400	Active TSS	HSMM	muscle
20	chr1:47902200-47904400	Active TSS	NHLF	lung
21	chr1:47902200-47904600	Active TSS	Small Intestine	intestine
22	chr1:47902200-47905000	Active TSS	Aorta	Aorta
23	chr1:47902200-47906000	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr1:47902400-47903400	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr1:47902400-47903400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:47902400-47903400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
27	chr1:47902400-47903600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
28	chr1:47902400-47903800	Active TSS	Esophagus	oesophagus
29	chr1:47902400-47903800	Active TSS	Dnd41	blood
30	chr1:47902400-47904000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:47902400-47904000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:47902400-47904000	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr1:47902400-47904400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
34	chr1:47902400-47904400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
35	chr1:47902400-47904400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
36	chr1:47902400-47904600	Bivalent Enhancer	Fetal Brain Male	brain
37	chr1:47902400-47904800	Active TSS	Ovary	ovary
38	chr1:47902600-47903400	Active TSS	Thymus	Thymus
39	chr1:47902600-47903600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:47902600-47903600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:47902600-47903600	Active TSS	Brain Substantia Nigra	brain
42	chr1:47902600-47904000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:47902600-47904000	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:47902600-47904000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:47902600-47904000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:47902600-47904000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:47902600-47904000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:47902600-47904000	Bivalent/Poised TSS	Left Ventricle	heart
49	chr1:47902600-47904000	Active TSS	GM12878-XiMat	blood
50	chr1:47902600-47904200	Active TSS	Muscle Satellite Cultured Cells	--

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