Variant report

Variant	rs1779860
Chromosome Location	chr1:61544080-61544081
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	MYC	chr1:61542384-61544453	K562	blood:	n/a	chr1:61542722-61542731 chr1:61543808-61543818
2	SP1	chr1:61542292-61544112	HCT-116	colon:	n/a	chr1:61543811-61543820 chr1:61543809-61543821 chr1:61543810-61543820 chr1:61543811-61543820 chr1:61542765-61542776 chr1:61543810-61543820 chr1:61543760-61543781 chr1:61543809-61543821 chr1:61543806-61543820 chr1:61543810-61543819 chr1:61542733-61542744 chr1:61542769-61542783
3	MAX	chr1:61542241-61544498	NB4	blood:	n/a	chr1:61542722-61542731 chr1:61543808-61543818
4	HCFC1	chr1:61542489-61544154	K562	blood:	n/a	n/a
5	NRF1	chr1:61542261-61544243	SK-N-SH	brain:	n/a	chr1:61543810-61543819
6	TEAD4	chr1:61543249-61544264	K562	blood:	n/a	chr1:61544090-61544099
7	GATA1	chr1:61543493-61544273	PBDE	blood:	n/a	n/a
8	RCOR1	chr1:61542288-61544101	K562	blood:	n/a	n/a
9	NFYA	chr1:61542558-61544115	K562	blood:	n/a	chr1:61542712-61542727 chr1:61543759-61543777 chr1:61542712-61542727 chr1:61542713-61542727
10	TBP	chr1:61542472-61544262	Hela-S3	cervix:	n/a	n/a
11	MXI1	chr1:61543691-61544452	K562	blood:	n/a	n/a
12	POLR2A	chr1:61543453-61544144	PFSK-1	brain:	n/a	n/a
13	KAP1	chr1:61541845-61544127	U2OS	brain:	n/a	n/a
14	MAFK	chr1:61542566-61544565	K562	blood:	n/a	chr1:61544177-61544191 chr1:61543550-61543561 chr1:61543550-61543565 chr1:61544174-61544194 chr1:61543551-61543562 chr1:61544176-61544192 chr1:61543549-61543563 chr1:61543550-61543561 chr1:61544482-61544496
15	CEBPB	chr1:61543755-61544166	K562	blood:	n/a	n/a
16	CHD2	chr1:61542526-61544209	K562	blood:	n/a	n/a
17	MYC	chr1:61543499-61544164	MCF10A-Er-Src	breast:	n/a	chr1:61543808-61543818
18	POLR2A	chr1:61542133-61544100	MCF10A-Er-Src	breast:	n/a	n/a
19	MAFK	chr1:61542447-61544306	HepG2	liver:	n/a	chr1:61544177-61544191 chr1:61543550-61543561 chr1:61543550-61543565 chr1:61544174-61544194 chr1:61543551-61543562 chr1:61544176-61544192 chr1:61543549-61543563 chr1:61543550-61543561
20	EP300	chr1:61543415-61544374	GM12878	blood:	n/a	n/a
21	TBL1XR1	chr1:61542246-61544602	K562	blood:	n/a	n/a
22	TEAD4	chr1:61543629-61544243	ECC-1	luminal epithelium:	n/a	chr1:61544090-61544099
23	SIN3A	chr1:61542280-61544115	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr1:61543299-61544083	SK-N-MC	brain:	n/a	n/a
25	POLR2A	chr1:61542247-61544221	SK-N-MC	brain:	n/a	n/a
26	ELF1	chr1:61543508-61544125	K562	blood:	n/a	chr1:61543888-61543899 chr1:61543888-61543899
27	CUX1	chr1:61542089-61544438	K562	blood:	n/a	chr1:61542919-61542928
28	RFX5	chr1:61543987-61544235	K562	blood:	n/a	n/a
29	MYC	chr1:61542313-61544424	NB4	blood:	n/a	chr1:61542722-61542731 chr1:61543808-61543818
30	MAFK	chr1:61542326-61544277	HepG2	liver:	n/a	chr1:61544177-61544191 chr1:61543550-61543561 chr1:61543550-61543565 chr1:61544174-61544194 chr1:61543551-61543562 chr1:61544176-61544192 chr1:61543549-61543563 chr1:61543550-61543561
31	SPI1	chr1:61543532-61544098	HL-60	blood:	n/a	chr1:61543811-61543824
32	STAT3	chr1:61543401-61544347	MCF10A-Er-Src	breast:	n/a	chr1:61543999-61544010 chr1:61543812-61543824
33	PBX3	chr1:61543424-61544085	SK-N-SH	brain:	n/a	chr1:61543747-61543767
34	POLR2A	chr1:61543433-61544088	PANC-1	pancreas:	n/a	n/a
35	ZNF384	chr1:61542477-61544199	K562	blood:	n/a	n/a
36	SP1	chr1:61542220-61544178	HCT-116	colon:	n/a	chr1:61543811-61543820 chr1:61543809-61543821 chr1:61543810-61543820 chr1:61543811-61543820 chr1:61542765-61542776 chr1:61543810-61543820 chr1:61543760-61543781 chr1:61543809-61543821 chr1:61543806-61543820 chr1:61543810-61543819 chr1:61542733-61542744 chr1:61542769-61542783
37	MAFK	chr1:61542342-61544341	Hela-S3	cervix:	n/a	chr1:61544177-61544191 chr1:61543550-61543561 chr1:61543550-61543565 chr1:61544174-61544194 chr1:61543551-61543562 chr1:61544176-61544192 chr1:61543549-61543563 chr1:61543550-61543561
38	NFYA	chr1:61542548-61544129	Hela-S3	cervix:	n/a	chr1:61542712-61542727 chr1:61543759-61543777 chr1:61542712-61542727 chr1:61542713-61542727
39	ELF1	chr1:61543633-61544090	MCF-7	breast:	n/a	chr1:61543888-61543899 chr1:61543888-61543899
40	BHLHE40	chr1:61543632-61544603	K562	blood:	n/a	n/a
41	IRF1	chr1:61542398-61544351	K562	blood:	n/a	chr1:61542486-61542497 chr1:61542485-61542499 chr1:61542483-61542497 chr1:61542484-61542501 chr1:61542483-61542503 chr1:61543809-61543823
42	ELF1	chr1:61543507-61544117	MCF-7	breast:	n/a	chr1:61543888-61543899 chr1:61543888-61543899
43	RCOR1	chr1:61543439-61544363	K562	blood:	n/a	n/a
44	ELF1	chr1:61542469-61544179	SK-N-SH	brain:	n/a	chr1:61543172-61543183 chr1:61543888-61543899 chr1:61543172-61543183 chr1:61543888-61543899
45	MXI1	chr1:61542515-61544298	Hela-S3	cervix:	n/a	n/a
46	MAFF	chr1:61542495-61544471	K562	blood:	n/a	chr1:61543548-61543566 chr1:61544177-61544191
47	TEAD4	chr1:61542288-61544513	K562	blood:	n/a	chr1:61544090-61544099
48	TCF7L2	chr1:61543532-61544088	Hela-S3	cervix:	n/a	n/a
49	MXI1	chr1:61541849-61550122	SK-N-SH	brain:	n/a	chr1:61544448-61544463
50	IRF3	chr1:61543463-61544210	Hela-S3	cervix:	n/a	chr1:61543809-61543823

No.	Distal block	Cell Line	Cell type
1	chr1:61513320..61528030-chr1:61539604..61553659,57	K562	blood:
2	chr1:61443627..61446348-chr1:61543642..61545335,2	K562	blood:
3	chr1:61542330..61544925-chr1:61552645..61554391,2	MCF-7	breast:
4	chr1:61512478..61530748-chr1:61539371..61553659,68	K562	blood:
5	chr1:61541387..61547328-chr1:61547444..61551394,9	MCF-7	breast:
6	chr1:61543393..61545559-chr1:61710850..61712816,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-INADL-7	chr1:61542791-61544920	NONHSAT003598

Variant related genes	Relation type
NFIA	TF binding region
ENSG00000162599	Chromatin interaction
ENSG00000263380	Chromatin interaction

rs_ID	r²[population]
rs11811322	1.00[AMR][1000 genomes]
rs1694221	1.00[AMR][1000 genomes]
rs1777535	1.00[AMR][1000 genomes]
rs1777542	1.00[AMR][1000 genomes]
rs1779852	1.00[AMR][1000 genomes]
rs1779853	1.00[AMR][1000 genomes]
rs1779859	1.00[AMR][1000 genomes]
rs1779862	1.00[AMR][1000 genomes]
rs1779863	1.00[AMR][1000 genomes]
rs544496	1.00[AMR][1000 genomes]
rs61131876	1.00[AMR][1000 genomes]
rs667553	1.00[AMR][1000 genomes]
rs72911911	1.00[AMR][1000 genomes]
rs72911916	1.00[AMR][1000 genomes]
rs72911921	1.00[AMR][1000 genomes]

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61542000-61544400	Active TSS	Thymus	Thymus
2	chr1:61542000-61544800	Active TSS	Right Atrium	heart
3	chr1:61542200-61544200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:61542200-61544200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:61542200-61544200	Active TSS	Aorta	Aorta
6	chr1:61542200-61544200	Active TSS	Fetal Intestine Large	intestine
7	chr1:61542200-61544200	Active TSS	Psoas Muscle	Psoas
8	chr1:61542200-61544200	Active TSS	Right Ventricle	heart
9	chr1:61542200-61544200	Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr1:61542200-61544400	Active TSS	Colonic Mucosa	Colon
11	chr1:61542200-61544400	Active TSS	Fetal Muscle Leg	muscle
12	chr1:61542400-61544200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:61542400-61544200	Active TSS	Brain Angular Gyrus	brain
14	chr1:61542400-61544200	Active TSS	Stomach Mucosa	stomach
15	chr1:61542400-61544400	Active TSS	Left Ventricle	heart
16	chr1:61542600-61544200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:61542600-61544200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:61542600-61544200	Active TSS	Brain Substantia Nigra	brain
19	chr1:61542600-61544200	Active TSS	Duodenum Mucosa	Duodenum
20	chr1:61542600-61544200	Active TSS	Fetal Heart	heart
21	chr1:61542600-61544200	Active TSS	Fetal Intestine Small	intestine
22	chr1:61542600-61544200	Active TSS	Fetal Stomach	stomach
23	chr1:61542600-61544200	Active TSS	HSMMtube	muscle
24	chr1:61542800-61544200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:61542800-61544200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:61542800-61544200	Active TSS	Fetal Thymus	thymus
27	chr1:61542800-61544400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:61542800-61544400	Active TSS	Fetal Muscle Trunk	muscle
29	chr1:61542800-61544800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:61543000-61544200	Active TSS	Primary T cells fromperipheralblood	blood
31	chr1:61543000-61544200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:61543000-61544400	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr1:61543200-61544200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr1:61543200-61544400	Weak transcription	Gastric	stomach
35	chr1:61543200-61547200	Weak transcription	Pancreas	Pancrea
36	chr1:61543200-61547400	Weak transcription	Lung	lung
37	chr1:61543400-61544600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:61543400-61544800	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr1:61543400-61544800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:61543600-61544200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr1:61543600-61544400	Weak transcription	Small Intestine	intestine
42	chr1:61543800-61544200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
43	chr1:61543800-61544200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr1:61543800-61544200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:61543800-61544200	Flanking Active TSS	Liver	Liver
46	chr1:61543800-61544200	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr1:61543800-61544200	Flanking Active TSS	Fetal Brain Female	brain
48	chr1:61543800-61544200	Bivalent/Poised TSS	GM12878-XiMat	blood
49	chr1:61543800-61544400	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr1:61543800-61544400	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links