Variant report

Variant	rs375363239
Chromosome Location	chr1:225841609-225841610
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	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	YY1	chr1:225841539-225841806	SK-N-SH_RA	brain:	n/a	chr1:225841789-225841798
8	POLR2A	chr1:225840922-225841761	A549	lung:	n/a	n/a
9	POLR2A	chr1:225840488-225841771	A549	lung:	n/a	n/a
10	RAD21	chr1:225841139-225841860	IMR90	lung:	n/a	chr1:225841786-225841796
11	MXI1	chr1:225840342-225841696	HepG2	liver:	n/a	n/a
12	MAX	chr1:225841118-225841627	MCF-7	breast:	n/a	n/a
13	TCF7L2	chr1:225840608-225841770	HCT-116	colon:	n/a	n/a
14	TAF7	chr1:225840112-225841860	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr1:225840524-225841813	HepG2	liver:	n/a	n/a
16	CREB1	chr1:225840439-225841956	HepG2	liver:	n/a	chr1:225841631-225841644
17	POLR2A	chr1:225841179-225842118	HepG2	liver:	n/a	n/a
18	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
19	POLR2A	chr1:225839670-225841962	H1-hESC	embryonic stem cell:	n/a	n/a
20	GATA3	chr1:225841503-225841925	T-47D	breast:	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	CTCF	chr1:225841460-225841610	A549	lung:	n/a	n/a
27	POLR2A	chr1:225839685-225841842	ECC-1	luminal epithelium:	n/a	n/a
28	MAZ	chr1:225840422-225841675	HepG2	liver:	n/a	n/a
29	REST	chr1:225841059-225842101	A549	lung:	n/a	chr1:225841262-225841275
30	POLR2A	chr1:225839665-225842385	H1-hESC	embryonic stem cell:	n/a	n/a
31	HA-E2F1	chr1:225841226-225841967	MCF-7	breast:	n/a	chr1:225841789-225841801 chr1:225841481-225841491 chr1:225841789-225841798
32	TBP	chr1:225841261-225841746	HepG2	liver:	n/a	n/a
33	POLR2A	chr1:225840417-225841831	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr1:225840499-225841990	HUVEC	blood vessel:	n/a	n/a
35	ETS1	chr1:225841045-225841777	A549	lung:	n/a	chr1:225841204-225841217 chr1:225841076-225841087 chr1:225841115-225841126 chr1:225841108-225841121
36	POLR2A	chr1:225840189-225841841	A549	lung:	n/a	n/a
37	SIN3AK20	chr1:225841448-225841753	A549	lung:	n/a	n/a
38	TAF1	chr1:225840107-225841815	ECC-1	luminal epithelium:	n/a	n/a
39	KAP1	chr1:225841342-225841869	HEK293	kidney:	n/a	n/a
40	POLR2A	chr1:225838660-225844042	MCF10A-Er-Src	breast:	n/a	n/a
41	ZBTB7A	chr1:225839959-225841851	ECC-1	luminal epithelium:	n/a	chr1:225840325-225840336
42	FOXP2	chr1:225840591-225841775	PFSK-1	brain:	n/a	n/a
43	FOXP2	chr1:225841526-225841802	SK-N-MC	brain:	n/a	n/a
44	MAX	chr1:225840533-225841815	ECC-1	luminal epithelium:	n/a	n/a
45	FOS	chr1:225841556-225841737	MCF10A-Er-Src	breast:	n/a	n/a
46	YY1	chr1:225841354-225842374	SK-N-SH	brain:	n/a	chr1:225842133-225842145 chr1:225841471-225841485 chr1:225841789-225841798 chr1:225842135-225842145
47	BCL3	chr1:225841233-225841949	A549	lung:	n/a	chr1:225841480-225841493
48	POLR2A	chr1:225840071-225843898	PANC-1	pancreas:	n/a	n/a
49	POLR2A	chr1:225840925-225841866	H1-hESC	embryonic stem cell:	n/a	n/a
50	CHD2	chr1:225840957-225841932	H1-hESC	embryonic stem cell:	n/a	chr1:225841790-225841800

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:225841605-225841655	Caco-2	colon:	n/a
2	chr1:225841605-225841655	Jurkat	blood:	n/a
3	chr1:225841605-225841655	HNPCEpiC	eye:	n/a
4	chr1:225841605-225841655	HepG2	liver:	n/a
5	chr1:225841605-225841655	K562	blood:	n/a
6	chr1:225841605-225841655	SAEC	small airway:	n/a
7	chr1:225841605-225841655	BE2_C	brain:	n/a
8	chr1:225841605-225841655	PANC-1	pancreas:	n/a
9	chr1:225841605-225841655	HRE	kidney:	n/a
10	chr1:225841605-225841655	HCT-116	colon:	n/a
11	chr1:225841605-225841655	Hepatocyte	liver:	n/a
12	chr1:225841605-225841655	HMEC	breast:	n/a
13	chr1:225841605-225841655	AoSMC	blood vessel:	n/a
14	chr1:225841605-225841655	BJ	skin:	n/a
15	chr1:225841605-225841655	SK-N-SH	brain:	n/a
16	chr1:225841605-225841655	GM12892	blood:	n/a
17	chr1:225841605-225841655	HRPEpiC	eye:	n/a
18	chr1:225841605-225841655	NB4	blood:	n/a
19	chr1:225841605-225841655	HL-60	blood:	n/a
20	chr1:225841605-225841655	HCPEpiC	choroid plexus:	n/a
21	chr1:225841605-225841655	ovcar-3	ovarian:	n/a
22	chr1:225841605-225841655	HUVEC	blood vessel:	n/a
23	chr1:225841605-225841655	HPAEpiC	pulmonary alveolar:	n/a
24	chr1:225841605-225841655	AG09319	gingival:	n/a
25	chr1:225841605-225841655	NT2-D1	testis:	n/a
26	chr1:225841605-225841655	HIPEpiC	eye:	n/a
27	chr1:225841605-225841655	HAEpiC	amniotic membrane:	n/a
28	chr1:225841605-225841655	NHBE	bronchial:	n/a
29	chr1:225841605-225841655	PFSK-1	brain:	n/a
30	chr1:225841605-225841655	NHDF-neo	bronchial:	n/a
31	chr1:225841605-225841655	CMK	blood:	n/a
32	chr1:225841605-225841655	ProgFib	skin:	n/a
33	chr1:225841605-225841655	MCF10A-Er-Src	breast:	n/a
34	chr1:225841605-225841655	ECC-1	luminal epithelium:	n/a
35	chr1:225841605-225841655	T-47D	breast:	n/a
36	chr1:225841605-225841655	HCM	heart:	n/a
37	chr1:225841605-225841655	GM06990	blood:	n/a
38	chr1:225841605-225841655	A549	lung:	n/a
39	chr1:225841605-225841655	PrEC	prostate:	n/a
40	chr1:225841605-225841655	MCF-7	breast:	n/a
41	chr1:225841605-225841655	U87	brain:	n/a
42	chr1:225841605-225841655	GM12891	blood:	n/a
43	chr1:225841605-225841655	AG04449	skin:	fetal
44	chr1:225841605-225841655	AG09309	skin:	n/a
45	chr1:225841605-225841655	GM12878	blood:	n/a
46	chr1:225841605-225841655	LNCaP	prostate:	n/a
47	chr1:225841605-225841655	SK-N-MC	brain:	n/a
48	chr1:225841605-225841655	SKMC	muscle:	n/a
49	chr1:225841605-225841655	HRCEpiC	kidney:	n/a
50	chr1:225841605-225841655	IMR90	lung:	fetal

No.	Distal block	Cell Line	Cell type
1	chr1:225841590..225843627-chr1:225887293..225890031,4	MCF-7	breast:
2	chr1:225839962..225842492-chr1:226249684..226252539,2	MCF-7	breast:
3	chr1:225839775..225842863-chr1:225886341..225888955,3	MCF-7	breast:
4	chr1:225766054..225768167-chr1:225839556..225842131,2	MCF-7	breast:
5	chr1:225841158..225843185-chr1:226308432..226310542,2	MCF-7	breast:
6	chr1:225839309..225842570-chr1:226062972..226068660,6	MCF-7	breast:
7	chr1:225840996..225843850-chr1:225947438..225950251,2	MCF-7	breast:
8	chr1:225839340..225843768-chr1:225964006..225968066,9	MCF-7	breast:
9	chr1:225837738..225841787-chr1:225965241..225967265,3	MCF-7	breast:
10	chr1:225692749..225695160-chr1:225840876..225842568,2	MCF-7	breast:

Variant related genes	Relation type
ENAH	TF binding region
ENAH	CpG island
ENSG00000196187	Chromatin interaction
ENSG00000163041	Chromatin interaction
ENSG00000227496	Chromatin interaction
ENSG00000143742	Chromatin interaction
ENSG00000154380	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	chr1:225837600-225841800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:225837600-225842000	Active TSS	Fetal Lung	lung
12	chr1:225837600-225842000	Active TSS	Rectal Smooth Muscle	rectum
13	chr1:225837600-225842400	Active TSS	H1 Cell Line	embryonic stem cell
14	chr1:225838000-225841800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:225838000-225841800	Active TSS	Colon Smooth Muscle	Colon
16	chr1:225838000-225842000	Active TSS	Fetal Stomach	stomach
17	chr1:225838000-225842200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:225838000-225842400	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr1:225838000-225842400	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr1:225838000-225842800	Active TSS	A549	lung
21	chr1:225838200-225841800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:225838200-225841800	Active TSS	Muscle Satellite Cultured Cells	--
23	chr1:225838200-225842000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:225838200-225842000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:225838200-225842000	Active TSS	NH-A	brain
26	chr1:225838200-225842200	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr1:225838200-225842200	Active TSS	HSMM	muscle
28	chr1:225838200-225842200	Active TSS	HSMMtube	muscle
29	chr1:225838200-225842400	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr1:225838200-225842400	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr1:225838200-225842400	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr1:225838200-225842800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:225838400-225842000	Active TSS	NHDF-Ad	bronchial
34	chr1:225838400-225842200	Active TSS	H9 Cell Line	embryonic stem cell
35	chr1:225838400-225842200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:225838600-225842000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:225838600-225842000	Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr1:225838600-225842000	Active TSS	Fetal Kidney	kidney
39	chr1:225838600-225842000	Active TSS	HMEC	breast
40	chr1:225838600-225842200	Active TSS	Fetal Muscle Trunk	muscle
41	chr1:225838800-225842000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:225838800-225842200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr1:225838800-225842200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:225838800-225842200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:225838800-225842200	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr1:225839000-225841800	Active TSS	NHEK	skin
47	chr1:225839000-225842000	Active TSS	Brain Cingulate Gyrus	brain
48	chr1:225839000-225842200	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr1:225839200-225841800	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr1:225839200-225841800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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