Variant report

Variant	rs558264608
Chromosome Location	chr1:225841420-225841421
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	chr1:225840354-225841982	SK-N-MC	brain:	n/a	n/a
2	EP300	chr1:225840461-225841969	ECC-1	luminal epithelium:	n/a	chr1:225840646-225840655 chr1:225841036-225841045 chr1:225841039-225841048 chr1:225840568-225840581 chr1:225841481-225841497 chr1:225841475-225841491
3	MAZ	chr1:225839134-225842062	IMR90	lung:	n/a	chr1:225840253-225840263
4	POLR2A	chr1:225840543-225841757	A549	lung:	n/a	n/a
5	POLR2A	chr1:225840922-225841901	U87	brain:	n/a	n/a
6	TAF7	chr1:225841117-225841709	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:225840922-225841761	A549	lung:	n/a	n/a
8	POLR2A	chr1:225840488-225841771	A549	lung:	n/a	n/a
9	RAD21	chr1:225841139-225841860	IMR90	lung:	n/a	chr1:225841786-225841796
10	MXI1	chr1:225840342-225841696	HepG2	liver:	n/a	n/a
11	MAX	chr1:225841118-225841627	MCF-7	breast:	n/a	n/a
12	TCF7L2	chr1:225840608-225841770	HCT-116	colon:	n/a	n/a
13	TAF7	chr1:225840112-225841860	H1-hESC	embryonic stem cell:	n/a	n/a
14	REST	chr1:225841098-225841428	PANC-1	pancreas:	n/a	chr1:225841262-225841275
15	POLR2A	chr1:225840524-225841813	HepG2	liver:	n/a	n/a
16	NR3C1	chr1:225841032-225841485	A549	lung:	n/a	n/a
17	CREB1	chr1:225840439-225841956	HepG2	liver:	n/a	chr1:225841631-225841644
18	POLR2A	chr1:225841179-225842118	HepG2	liver:	n/a	n/a
19	SP1	chr1:225840598-225841903	A549	lung:	n/a	chr1:225841074-225841086 chr1:225840851-225840860 chr1:225841191-225841203 chr1:225840608-225840620 chr1:225841075-225841084 chr1:225840849-225840861 chr1:225840609-225840618 chr1:225841076-225841085 chr1:225841790-225841799 chr1:225841075-225841089 chr1:225841075-225841085 chr1:225840850-225840859 chr1:225841788-225841800 chr1:225840605-225840619 chr1:225841074-225841086 chr1:225841785-225841799 chr1:225841790-225841799 chr1:225841789-225841798 chr1:225840846-225840860 chr1:225841788-225841800 chr1:225840894-225840908 chr1:225841075-225841085 chr1:225841193-225841202 chr1:225840849-225840861 chr1:225841075-225841084
20	POLR2A	chr1:225839670-225841962	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr1:225840534-225841806	SK-N-SH	brain:	n/a	n/a
22	CHD2	chr1:225840615-225841753	HepG2	liver:	n/a	chr1:225840811-225840821
23	POLR2A	chr1:225840472-225841800	MCF-7	breast:	n/a	n/a
24	POLR2A	chr1:225841393-225841832	SK-N-MC	brain:	n/a	n/a
25	MAX	chr1:225841124-225841823	A549	lung:	n/a	n/a
26	POLR2A	chr1:225839685-225841842	ECC-1	luminal epithelium:	n/a	n/a
27	MAZ	chr1:225840422-225841675	HepG2	liver:	n/a	n/a
28	REST	chr1:225841059-225842101	A549	lung:	n/a	chr1:225841262-225841275
29	POLR2A	chr1:225839665-225842385	H1-hESC	embryonic stem cell:	n/a	n/a
30	HA-E2F1	chr1:225841226-225841967	MCF-7	breast:	n/a	chr1:225841789-225841801 chr1:225841481-225841491 chr1:225841789-225841798
31	TBP	chr1:225841261-225841746	HepG2	liver:	n/a	n/a
32	POLR2A	chr1:225840417-225841831	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr1:225840499-225841990	HUVEC	blood vessel:	n/a	n/a
34	ETS1	chr1:225841045-225841777	A549	lung:	n/a	chr1:225841204-225841217 chr1:225841076-225841087 chr1:225841115-225841126 chr1:225841108-225841121
35	POLR2A	chr1:225840189-225841841	A549	lung:	n/a	n/a
36	POLR2A	chr1:225840535-225841439	HCT-116	colon:	n/a	n/a
37	TAF1	chr1:225840107-225841815	ECC-1	luminal epithelium:	n/a	n/a
38	KAP1	chr1:225841342-225841869	HEK293	kidney:	n/a	n/a
39	POLR2A	chr1:225838660-225844042	MCF10A-Er-Src	breast:	n/a	n/a
40	ZBTB7A	chr1:225839959-225841851	ECC-1	luminal epithelium:	n/a	chr1:225840325-225840336
41	FOXP2	chr1:225840591-225841775	PFSK-1	brain:	n/a	n/a
42	MAX	chr1:225840533-225841815	ECC-1	luminal epithelium:	n/a	n/a
43	YY1	chr1:225841354-225842374	SK-N-SH	brain:	n/a	chr1:225842133-225842145 chr1:225841471-225841485 chr1:225841789-225841798 chr1:225842135-225842145
44	BCL3	chr1:225841233-225841949	A549	lung:	n/a	chr1:225841480-225841493
45	YY1	chr1:225841058-225841460	HCT-116	colon:	n/a	chr1:225841119-225841130 chr1:225841076-225841085
46	POLR2A	chr1:225840071-225843898	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr1:225840925-225841866	H1-hESC	embryonic stem cell:	n/a	n/a
48	CHD2	chr1:225840957-225841932	H1-hESC	embryonic stem cell:	n/a	chr1:225841790-225841800
49	JUND	chr1:225840537-225841902	A549	lung:	n/a	chr1:225841209-225841218
50	SIN3AK20	chr1:225840023-225841860	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:225839962..225842492-chr1:226249684..226252539,2	MCF-7	breast:
2	chr1:225839775..225842863-chr1:225886341..225888955,3	MCF-7	breast:
3	chr1:225766054..225768167-chr1:225839556..225842131,2	MCF-7	breast:
4	chr1:225841158..225843185-chr1:226308432..226310542,2	MCF-7	breast:
5	chr1:225839309..225842570-chr1:226062972..226068660,6	MCF-7	breast:
6	chr1:225840996..225843850-chr1:225947438..225950251,2	MCF-7	breast:
7	chr1:225839340..225843768-chr1:225964006..225968066,9	MCF-7	breast:
8	chr1:225837738..225841787-chr1:225965241..225967265,3	MCF-7	breast:
9	chr1:225692749..225695160-chr1:225840876..225842568,2	MCF-7	breast:

Variant related genes	Relation type
ENAH	TF binding region
ENSG00000227496	Chromatin interaction
ENSG00000154380	Chromatin interaction
ENSG00000196187	Chromatin interaction
ENSG00000143742	Chromatin interaction
ENSG00000163041	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	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv3435512	chr1:225838929-225842227	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	esv3329174	chr1:225839754-225842702	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	esv3323320	chr1:225840179-225841727	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 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	chr1:225836200-225842000	Active TSS	Aorta	Aorta
2	chr1:225836600-225842200	Active TSS	Right Ventricle	heart
3	chr1:225836600-225842200	Active TSS	Stomach Smooth Muscle	stomach
4	chr1:225836800-225842200	Active TSS	NHLF	lung
5	chr1:225837000-225842000	Active TSS	Ovary	ovary
6	chr1:225837000-225842800	Active TSS	Psoas Muscle	Psoas
7	chr1:225837200-225841800	Active TSS	Osteobl	bone
8	chr1:225837200-225842800	Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr1:225837400-225842200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:225837600-225841600	Active TSS	Fetal Muscle Leg	muscle
11	chr1:225837600-225841800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:225837600-225842000	Active TSS	Fetal Lung	lung
13	chr1:225837600-225842000	Active TSS	Rectal Smooth Muscle	rectum
14	chr1:225837600-225842400	Active TSS	H1 Cell Line	embryonic stem cell
15	chr1:225838000-225841800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:225838000-225841800	Active TSS	Colon Smooth Muscle	Colon
17	chr1:225838000-225842000	Active TSS	Fetal Stomach	stomach
18	chr1:225838000-225842200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:225838000-225842400	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr1:225838000-225842400	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr1:225838000-225842800	Active TSS	A549	lung
22	chr1:225838200-225841600	Active TSS	Fetal Brain Female	brain
23	chr1:225838200-225841800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:225838200-225841800	Active TSS	Muscle Satellite Cultured Cells	--
25	chr1:225838200-225842000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:225838200-225842000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:225838200-225842000	Active TSS	NH-A	brain
28	chr1:225838200-225842200	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr1:225838200-225842200	Active TSS	HSMM	muscle
30	chr1:225838200-225842200	Active TSS	HSMMtube	muscle
31	chr1:225838200-225842400	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr1:225838200-225842400	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr1:225838200-225842400	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr1:225838200-225842800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:225838400-225842000	Active TSS	NHDF-Ad	bronchial
36	chr1:225838400-225842200	Active TSS	H9 Cell Line	embryonic stem cell
37	chr1:225838400-225842200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:225838600-225842000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:225838600-225842000	Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr1:225838600-225842000	Active TSS	Fetal Kidney	kidney
41	chr1:225838600-225842000	Active TSS	HMEC	breast
42	chr1:225838600-225842200	Active TSS	Fetal Muscle Trunk	muscle
43	chr1:225838800-225841600	Active TSS	Duodenum Mucosa	Duodenum
44	chr1:225838800-225842000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:225838800-225842200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr1:225838800-225842200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:225838800-225842200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:225838800-225842200	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr1:225839000-225841800	Active TSS	NHEK	skin
50	chr1:225839000-225842000	Active TSS	Brain Cingulate Gyrus	brain

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