Variant report

Variant	rs2840947
Chromosome Location	chr1:225888224-225888225
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	MAX	chr1:225887554-225889050	SK-N-SH	brain:	n/a	n/a
2	EP300	chr1:225887777-225888444	HepG2	liver:	n/a	chr1:225888066-225888076 chr1:225888230-225888244
3	BCL3	chr1:225887589-225888483	A549	lung:	n/a	n/a
4	MAX	chr1:225887673-225888436	HepG2	liver:	n/a	n/a
5	EP300	chr1:225887727-225888435	HepG2	liver:	n/a	chr1:225888066-225888076 chr1:225888230-225888244
6	NR3C1	chr1:225887769-225888560	ECC-1	luminal epithelium:	n/a	chr1:225887922-225887948 chr1:225887922-225887948 chr1:225887926-225887944 chr1:225887928-225887943 chr1:225887922-225887948 chr1:225887922-225887948
7	FOS	chr1:225887785-225888484	MCF10A-Er-Src	breast:	n/a	chr1:225887940-225887949
8	MXI1	chr1:225887753-225888345	HepG2	liver:	n/a	n/a
9	EP300	chr1:225887635-225888416	Hela-S3	cervix:	n/a	chr1:225888066-225888076 chr1:225888230-225888244
10	SIN3AK20	chr1:225887722-225888326	MCF-7	breast:	n/a	n/a
11	FOXA2	chr1:225887688-225888459	A549	lung:	n/a	chr1:225888067-225888079
12	FOSL2	chr1:225887653-225888644	SK-N-SH	brain:	n/a	chr1:225887940-225887949
13	CEBPB	chr1:225887754-225888623	ECC-1	luminal epithelium:	n/a	chr1:225888229-225888242 chr1:225888024-225888037
14	NR3C1	chr1:225887948-225888564	ECC-1	luminal epithelium:	n/a	n/a
15	FOSL2	chr1:225887870-225888357	HepG2	liver:	n/a	chr1:225887940-225887949
16	JUN	chr1:225887841-225888379	HUVEC	blood vessel:	n/a	chr1:225887940-225887949
17	SMARCC1	chr1:225887626-225888748	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr1:225887424-225888556	SK-N-SH	brain:	n/a	n/a
19	STAT3	chr1:225887742-225888569	MCF10A-Er-Src	breast:	n/a	n/a
20	MBD4	chr1:225887848-225888423	HepG2	liver:	n/a	n/a
21	CEBPB	chr1:225887813-225888407	HepG2	liver:	n/a	chr1:225888229-225888242 chr1:225888024-225888037
22	EP300	chr1:225887270-225888711	A549	lung:	n/a	chr1:225888066-225888076 chr1:225888230-225888244
23	TCF12	chr1:225887511-225888684	A549	lung:	n/a	n/a
24	FOXM1	chr1:225887447-225888813	ECC-1	luminal epithelium:	n/a	n/a
25	EP300	chr1:225887765-225888678	ECC-1	luminal epithelium:	n/a	chr1:225888066-225888076 chr1:225888230-225888244
26	JUN	chr1:225887689-225888436	Hela-S3	cervix:	n/a	chr1:225887940-225887949
27	POLR2A	chr1:225887816-225888362	PANC-1	pancreas:	n/a	n/a
28	TEAD4	chr1:225887731-225888658	ECC-1	luminal epithelium:	n/a	n/a
29	TCF7L2	chr1:225887084-225888903	HCT-116	colon:	n/a	chr1:225887540-225887556 chr1:225887802-225887809 chr1:225887540-225887556
30	JUN	chr1:225887780-225888421	HepG2	liver:	n/a	chr1:225887940-225887949
31	USF1	chr1:225887753-225889385	HCT-116	colon:	n/a	n/a
32	RAD21	chr1:225887969-225888794	A549	lung:	n/a	n/a
33	E2F6	chr1:225887724-225888646	A549	lung:	n/a	n/a
34	MAX	chr1:225887650-225888493	SK-N-SH	brain:	n/a	n/a
35	PBX3	chr1:225887389-225888585	SK-N-SH	brain:	n/a	chr1:225887941-225887950
36	ESR1	chr1:225887971-225888447	ECC-1	luminal epithelium:	n/a	n/a
37	FOSL2	chr1:225887856-225888370	HepG2	liver:	n/a	chr1:225887940-225887949
38	EP300	chr1:225887721-225888457	SK-N-SH_RA	brain:	n/a	chr1:225888066-225888076 chr1:225888230-225888244
39	ELF1	chr1:225887702-225888373	A549	lung:	n/a	n/a
40	RCOR1	chr1:225887735-225888433	Hela-S3	cervix:	n/a	n/a
41	TEAD4	chr1:225887956-225888294	HepG2	liver:	n/a	n/a
42	FOXA2	chr1:225887748-225888511	A549	lung:	n/a	chr1:225888067-225888079
43	FOXA1	chr1:225887820-225888338	ECC-1	luminal epithelium:	n/a	chr1:225888067-225888079
44	FOS	chr1:225887687-225888491	MCF10A-Er-Src	breast:	n/a	chr1:225887940-225887949
45	POLR2A	chr1:225887893-225888356	HCT-116	colon:	n/a	n/a
46	SMC3	chr1:225887697-225888830	Hela-S3	cervix:	n/a	n/a
47	USF1	chr1:225887724-225888347	A549	lung:	n/a	n/a
48	POLR2A	chr1:225887155-225888332	HepG2	liver:	n/a	n/a
49	TEAD4	chr1:225887748-225888518	A549	lung:	n/a	n/a
50	E2F4	chr1:225887787-225888322	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225839775..225842863-chr1:225886341..225888955,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227496	TF binding region
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1764344	1.00[AMR][1000 genomes]
rs1771315	1.00[AMR][1000 genomes]
rs1876083	0.90[AFR][1000 genomes]
rs2131411	1.00[AMR][1000 genomes]
rs2615062	0.87[AFR][1000 genomes]
rs2615065	1.00[AMR][1000 genomes]
rs2615072	1.00[AMR][1000 genomes]
rs2639717	1.00[AMR][1000 genomes]
rs2657565	1.00[AMR][1000 genomes]
rs2769686	0.90[AFR][1000 genomes]
rs2794395	0.97[AFR][1000 genomes]
rs2794397	0.90[AFR][1000 genomes]
rs2840951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2840954	0.90[AFR][1000 genomes]
rs2840961	1.00[AMR][1000 genomes]
rs2840964	0.88[YRI][hapmap];0.91[AFR][1000 genomes]
rs4653641	1.00[AMR][1000 genomes]

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	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic 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 miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225875200-225898600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:225882200-225889600	Enhancers	Fetal Muscle Leg	muscle
3	chr1:225882400-225908000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:225886800-225888400	Enhancers	NH-A	brain
5	chr1:225887000-225888400	Enhancers	Stomach Smooth Muscle	stomach
6	chr1:225887000-225888400	Enhancers	HMEC	breast
7	chr1:225887000-225888600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:225887000-225888600	Enhancers	Fetal Stomach	stomach
9	chr1:225887000-225888800	Enhancers	HUVEC	blood vessel
10	chr1:225887000-225889000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:225887000-225889000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:225887000-225889200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:225887000-225889200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:225887000-225889200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:225887000-225889200	Enhancers	NHLF	lung
16	chr1:225887200-225888400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:225887200-225888400	Enhancers	Fetal Lung	lung
18	chr1:225887200-225888400	Flanking Active TSS	HepG2	liver
19	chr1:225887200-225888600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:225887200-225889200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:225887200-225889200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:225887200-225889400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:225887400-225888800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:225887600-225888400	Active TSS	Aorta	Aorta
25	chr1:225887600-225888800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:225887600-225888800	Flanking Active TSS	Hela-S3	cervix
27	chr1:225887600-225889600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:225887800-225888400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:225887800-225890600	Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr1:225888000-225888400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:225888000-225888400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:225888000-225888400	Enhancers	Muscle Satellite Cultured Cells	--
33	chr1:225888000-225888400	Enhancers	HSMM	muscle
34	chr1:225888000-225888400	Active TSS	HSMMtube	muscle
35	chr1:225888000-225888400	Enhancers	NHDF-Ad	bronchial
36	chr1:225888000-225888400	Enhancers	Osteobl	bone
37	chr1:225888000-225889600	Active TSS	Psoas Muscle	Psoas
38	chr1:225888000-225890200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:225888000-225891800	Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr1:225888200-225888400	Enhancers	NHEK	skin
41	chr1:225888200-225889000	Flanking Active TSS	A549	lung

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