Variant report

Variant	rs74077873
Chromosome Location	chr1:59280251-59280252
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	ZNF217	chr1:59279602-59280385	MCF-7	breast:	n/a	n/a
2	SIN3A	chr1:59280238-59280967	H1-hESC	embryonic stem cell:	n/a	chr1:59280669-59280678
3	POLR2A	chr1:59279717-59282573	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr1:59280152-59281691	H1-hESC	embryonic stem cell:	n/a	n/a
5	CEBPB	chr1:59279686-59282432	Hela-S3	cervix:	n/a	chr1:59279976-59279987 chr1:59279927-59279935
6	TCF7L2	chr1:59280126-59282415	HCT-116	colon:	n/a	n/a
7	TCF12	chr1:59279676-59282551	ECC-1	luminal epithelium:	n/a	chr1:59281207-59281217 chr1:59281032-59281041
8	EGR1	chr1:59279891-59280260	H1-hESC	embryonic stem cell:	n/a	chr1:59280060-59280074 chr1:59280060-59280073 chr1:59280063-59280072 chr1:59280059-59280074 chr1:59280061-59280072
9	EP300	chr1:59279720-59282623	ECC-1	luminal epithelium:	n/a	chr1:59281072-59281088 chr1:59282103-59282112 chr1:59281081-59281097 chr1:59282141-59282150 chr1:59281085-59281101 chr1:59281078-59281094 chr1:59281084-59281100 chr1:59281914-59281923
10	ELK4	chr1:59280077-59282480	Hela-S3	cervix:	n/a	n/a
11	SMARCB1	chr1:59279838-59282407	Hela-S3	cervix:	n/a	n/a
12	ELK1	chr1:59280122-59280506	Hela-S3	cervix:	n/a	n/a
13	MAZ	chr1:59279861-59282340	Hela-S3	cervix:	n/a	chr1:59281189-59281198 chr1:59280253-59280262
14	EGR1	chr1:59279749-59282500	HCT-116	colon:	n/a	chr1:59280835-59280857 chr1:59280060-59280074 chr1:59281051-59281065 chr1:59280060-59280073 chr1:59281909-59281922 chr1:59280063-59280072 chr1:59281097-59281110 chr1:59282140-59282149 chr1:59280839-59280852 chr1:59280831-59280844 chr1:59280838-59280853 chr1:59280839-59280853 chr1:59280059-59280074 chr1:59280061-59280072 chr1:59280839-59280852
15	GATA3	chr1:59279477-59280357	MCF-7	breast:	n/a	n/a
16	ZBTB7A	chr1:59279846-59281372	ECC-1	luminal epithelium:	n/a	n/a
17	CHD2	chr1:59280219-59282537	Hela-S3	cervix:	n/a	chr1:59281098-59281108 chr1:59280484-59280491
18	POLR2A	chr1:59279375-59282505	Hela-S3	cervix:	n/a	n/a
19	SIN3AK20	chr1:59279382-59282566	MCF-7	breast:	n/a	n/a
20	POLR2A	chr1:59280004-59281638	MCF-7	breast:	n/a	n/a
21	ELF1	chr1:59279700-59281342	MCF-7	breast:	n/a	chr1:59280132-59280144 chr1:59280462-59280474 chr1:59280297-59280306
22	TEAD4	chr1:59280149-59282391	ECC-1	luminal epithelium:	n/a	n/a
23	ELF1	chr1:59279859-59282614	HCT-116	colon:	n/a	chr1:59280132-59280144 chr1:59280462-59280474 chr1:59282105-59282114 chr1:59280297-59280306
24	NR2F2	chr1:59279472-59280330	MCF-7	breast:	n/a	n/a
25	STAT3	chr1:59280011-59280482	MCF10A-Er-Src	breast:	n/a	chr1:59280076-59280087 chr1:59280435-59280446 chr1:59280440-59280452
26	SMC3	chr1:59279900-59282839	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:59280144-59280623	HUVEC	blood vessel:	n/a	n/a
28	MAX	chr1:59279734-59282455	ECC-1	luminal epithelium:	n/a	chr1:59281189-59281198 chr1:59279816-59279832 chr1:59280253-59280262 chr1:59279827-59279834 chr1:59279823-59279838
29	POLR2A	chr1:59280091-59281654	Hela-S3	cervix:	n/a	n/a
30	SMARCC1	chr1:59280148-59282462	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr1:59280025-59282415	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr1:59280008-59282721	Hela-S3	cervix:	n/a	n/a
33	GABPA	chr1:59279720-59282526	MCF-7	breast:	n/a	chr1:59282130-59282139 chr1:59280289-59280298
34	POLR2A	chr1:59280179-59281509	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr1:59280181-59281617	HCT-116	colon:	n/a	n/a
36	TCF7L2	chr1:59280092-59282408	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr1:59279799-59281623	HCT-116	colon:	n/a	n/a
38	CTBP2	chr1:59280229-59282338	H1-hESC	embryonic stem cell:	n/a	n/a
39	STAT3	chr1:59279901-59280287	MCF10A-Er-Src	breast:	n/a	chr1:59280076-59280087
40	E2F6	chr1:59279958-59282375	H1-hESC	embryonic stem cell:	n/a	chr1:59282066-59282075 chr1:59280484-59280491 chr1:59281103-59281114 chr1:59281102-59281114
41	YY1	chr1:59280219-59280524	HCT-116	colon:	n/a	chr1:59280297-59280306
42	TCF12	chr1:59279813-59282627	ECC-1	luminal epithelium:	n/a	chr1:59281207-59281217 chr1:59281032-59281041
43	MAX	chr1:59280242-59281059	H1-hESC	embryonic stem cell:	n/a	chr1:59280253-59280262
44	NR2F2	chr1:59279428-59280330	MCF-7	breast:	n/a	n/a
45	ZBTB7A	chr1:59279856-59281230	ECC-1	luminal epithelium:	n/a	n/a
46	E2F4	chr1:59280199-59281611	Hela-S3	cervix:	n/a	chr1:59281103-59281114 chr1:59280484-59280491 chr1:59281102-59281114
47	NFIC	chr1:59280103-59282845	ECC-1	luminal epithelium:	n/a	n/a
48	EGR1	chr1:59279804-59281317	ECC-1	luminal epithelium:	n/a	chr1:59280835-59280857 chr1:59280060-59280074 chr1:59281051-59281065 chr1:59280060-59280073 chr1:59280063-59280072 chr1:59281097-59281110 chr1:59280839-59280852 chr1:59280831-59280844 chr1:59280838-59280853 chr1:59280839-59280853 chr1:59280059-59280074 chr1:59280061-59280072 chr1:59280839-59280852
49	MAX	chr1:59279489-59281410	MCF-7	breast:	n/a	chr1:59281189-59281198 chr1:59279816-59279832 chr1:59279719-59279728 chr1:59280253-59280262 chr1:59279827-59279834 chr1:59279823-59279838
50	POLR2A	chr1:59280193-59280553	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:59279129..59280859-chr1:59347455..59349368,2	K562	blood:
2	chr1:59279353..59283854-chr1:59287313..59291525,6	MCF-7	breast:
3	chr1:59245489..59255081-chr1:59277954..59283925,49	MCF-7	breast:
4	chr1:59280122..59283663-chr1:59349956..59353437,4	K562	blood:
5	chr1:59279109..59280911-chr1:59291721..59294413,2	MCF-7	breast:
6	chr1:59243405..59253875-chr1:59275011..59289058,45	MCF-7	breast:
7	chr1:59279369..59282052-chr1:60171210..60173225,3	MCF-7	breast:
8	chr1:59279457..59282981-chr1:59283687..59286487,4	K562	blood:
9	chr1:59279471..59282455-chr1:59331094..59333680,2	MCF-7	breast:
10	chr1:59243458..59255133-chr1:59272031..59283720,29	K562	blood:
11	chr1:59279921..59284497-chr1:59286325..59289409,4	K562	blood:
12	chr1:59280123..59281954-chr1:59395680..59397207,2	MCF-7	breast:
13	chr1:59279289..59281587-chr1:59349571..59351279,3	MCF-7	breast:
14	chr1:59279591..59281416-chr1:59282634..59284464,2	MCF-7	breast:
15	chr1:59279917..59282789-chr1:59295281..59296950,2	MCF-7	breast:
16	chr1:59091520..59094170-chr1:59279490..59282356,2	MCF-7	breast:
17	chr1:59280214..59283774-chr1:59346159..59349299,3	MCF-7	breast:
18	chr1:59280191..59282299-chr1:59284813..59286664,3	MCF-7	breast:
19	chr1:59279498..59283509-chr1:59392349..59395635,3	MCF-7	breast:
20	chr1:59279403..59281685-chr1:59758871..59761962,3	MCF-7	breast:
21	chr1:59279897..59281493-chr1:59891498..59894143,2	MCF-7	breast:
22	chr1:59279066..59281717-chr1:59892952..59895957,3	MCF-7	breast:
23	chr1:59279690..59282444-chr1:59408342..59410197,2	K562	blood:
24	chr1:59279994..59282679-chr1:59483503..59486905,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FGGY-5	chr1:59279801-59280409	NONHSAT003530

Variant related genes	Relation type
ENSG00000272226	TF binding region
ENSG00000177606	Chromatin interaction
ENSG00000230812	Chromatin interaction
ENSG00000234807	Chromatin interaction

rs_ID	r²[population]
rs12116591	1.00[AFR][1000 genomes]
rs4647011	0.82[AFR][1000 genomes]
rs57251170	1.00[AFR][1000 genomes]
rs57263270	0.94[AFR][1000 genomes]
rs58128095	0.94[AFR][1000 genomes]
rs60346486	1.00[AFR][1000 genomes]
rs74077827	1.00[AFR][1000 genomes]
rs74077829	1.00[AFR][1000 genomes]
rs74077830	1.00[AFR][1000 genomes]
rs74077832	1.00[AFR][1000 genomes]
rs74077834	1.00[AFR][1000 genomes]
rs74077835	1.00[AFR][1000 genomes]
rs74077837	1.00[AFR][1000 genomes]
rs74077838	1.00[AFR][1000 genomes]
rs74077839	1.00[AFR][1000 genomes]
rs74077840	1.00[AFR][1000 genomes]
rs74077844	1.00[AFR][1000 genomes]
rs74077847	1.00[AFR][1000 genomes]
rs74077850	1.00[AFR][1000 genomes]
rs74077851	0.94[AFR][1000 genomes]
rs74077854	1.00[AFR][1000 genomes]
rs74077855	1.00[AFR][1000 genomes]
rs74077856	1.00[AFR][1000 genomes]
rs74077866	1.00[AFR][1000 genomes]
rs74077868	1.00[AFR][1000 genomes]
rs74077870	1.00[AFR][1000 genomes]
rs74078326	1.00[AFR][1000 genomes]
rs74078327	1.00[AFR][1000 genomes]
rs74079803	1.00[AFR][1000 genomes]
rs74079808	0.94[AFR][1000 genomes]
rs74079815	0.88[AFR][1000 genomes]

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59254000-59281000	Weak transcription	Brain Substantia Nigra	brain
2	chr1:59265000-59280400	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:59268600-59280400	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:59274600-59281400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:59275200-59280600	Weak transcription	Fetal Brain Male	brain
6	chr1:59275400-59280800	Weak transcription	Fetal Heart	heart
7	chr1:59275600-59280400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:59275600-59280400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:59275600-59280400	Weak transcription	K562	blood
10	chr1:59275600-59280600	Weak transcription	NHDF-Ad	bronchial
11	chr1:59276000-59280400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:59276000-59280600	Weak transcription	HSMM	muscle
13	chr1:59276200-59280600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:59277200-59280600	Enhancers	Pancreas	Pancrea
15	chr1:59277600-59281200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:59277800-59280800	Enhancers	Primary T cells fromperipheralblood	blood
17	chr1:59277800-59280800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr1:59277800-59281000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:59278000-59280600	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr1:59278000-59280800	Enhancers	Primary B cells from peripheral blood	blood
21	chr1:59278000-59280800	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr1:59278000-59281000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr1:59278200-59280600	Enhancers	Primary B cells from cord blood	blood
24	chr1:59278200-59280800	Enhancers	Primary T cells from cord blood	blood
25	chr1:59278200-59280800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:59278200-59280800	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr1:59278200-59281000	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr1:59278200-59281000	Enhancers	Spleen	Spleen
29	chr1:59278400-59280600	Enhancers	GM12878-XiMat	blood
30	chr1:59278400-59280800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr1:59278600-59280400	Enhancers	A549	lung
32	chr1:59278600-59281000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:59278800-59280400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:59278800-59280600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:59278800-59280800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:59278800-59281200	Enhancers	Gastric	stomach
37	chr1:59279000-59281200	Enhancers	Placenta Amnion	Placenta Amnion
38	chr1:59279200-59280600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:59279200-59280600	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr1:59279200-59280800	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr1:59279200-59280800	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr1:59279400-59280400	Enhancers	Fetal Lung	lung
43	chr1:59279400-59280600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:59279400-59280600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:59279400-59280600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:59279400-59280600	Enhancers	Right Ventricle	heart
47	chr1:59279400-59280600	Weak transcription	Thymus	Thymus
48	chr1:59279400-59281600	Flanking Active TSS	Hela-S3	cervix
49	chr1:59279600-59280400	Enhancers	Fetal Muscle Trunk	muscle
50	chr1:59279600-59280400	Flanking Active TSS	HepG2	liver

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