Variant report

Variant	rs72900729
Chromosome Location	chr1:47185219-47185220
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	BHLHE40	chr1:47184534-47185722	K562	blood:	n/a	chr1:47184795-47184811
2	POLR2A	chr1:47184384-47185273	HUVEC	blood vessel:	n/a	n/a
3	GABPA	chr1:47184296-47185335	K562	blood:	n/a	chr1:47184949-47184958 chr1:47185020-47185029
4	GABPA	chr1:47184711-47185264	HL-60	blood:	n/a	chr1:47184949-47184958 chr1:47185020-47185029
5	MAX	chr1:47184441-47185221	H1-hESC	embryonic stem cell:	n/a	chr1:47185076-47185085
6	POLR2A	chr1:47183189-47185848	Hela-S3	cervix:	n/a	n/a
7	GABPA	chr1:47184475-47185320	HL-60	blood:	n/a	chr1:47184949-47184958 chr1:47185020-47185029
8	NR2F2	chr1:47184613-47185270	MCF-7	breast:	n/a	n/a
9	ZNF143	chr1:47184761-47185243	K562	blood:	n/a	chr1:47184804-47184814 chr1:47184906-47184916
10	POLR2A	chr1:47184376-47185281	SK-N-MC	brain:	n/a	n/a
11	SP1	chr1:47184496-47185274	K562	blood:	n/a	chr1:47184883-47184894 chr1:47184509-47184521 chr1:47184948-47184957 chr1:47184511-47184520 chr1:47184509-47184521 chr1:47185021-47185030 chr1:47184880-47184894 chr1:47184947-47184959 chr1:47184947-47184959 chr1:47184949-47184958 chr1:47184948-47184958 chr1:47184918-47184927 chr1:47184510-47184519 chr1:47184948-47184958 chr1:47184822-47184843 chr1:47184948-47184962 chr1:47184898-47184905 chr1:47184948-47184957 chr1:47185078-47185088
12	GATA2	chr1:47184761-47185665	HUVEC	blood vessel:	n/a	chr1:47185457-47185471 chr1:47185619-47185626
13	GATA3	chr1:47184603-47185219	MCF-7	breast:	n/a	n/a
14	MAZ	chr1:47184097-47185747	K562	blood:	n/a	chr1:47185076-47185085
15	POLR2A	chr1:47184530-47185374	MCF10A-Er-Src	breast:	n/a	n/a
16	ELF1	chr1:47184356-47185406	HCT-116	colon:	n/a	chr1:47184965-47184974 chr1:47184657-47184669 chr1:47184986-47184998
17	GATA3	chr1:47184969-47185678	MCF-7	breast:	n/a	chr1:47185619-47185626 chr1:47185461-47185469
18	JUN	chr1:47184687-47185292	K562	blood:	n/a	chr1:47184831-47184840 chr1:47184852-47184861 chr1:47184848-47184861
19	UBTF	chr1:47184225-47185248	K562	blood:	n/a	n/a
20	MAX	chr1:47184409-47185283	ECC-1	luminal epithelium:	n/a	chr1:47185076-47185085
21	ZC3H11A	chr1:47184806-47185246	K562	blood:	n/a	n/a
22	CREB1	chr1:47184514-47185234	HepG2	liver:	n/a	chr1:47184850-47184863
23	ELF1	chr1:47184466-47185254	SK-N-SH	brain:	n/a	chr1:47184965-47184974 chr1:47184657-47184669 chr1:47184986-47184998
24	MXI1	chr1:47184352-47185405	GM12878	blood:	n/a	n/a
25	MYC	chr1:47184344-47185417	NB4	blood:	n/a	chr1:47185076-47185085
26	POLR2A	chr1:47184288-47185248	NB4	blood:	n/a	n/a
27	SP1	chr1:47184397-47185431	HCT-116	colon:	n/a	chr1:47184883-47184894 chr1:47184509-47184521 chr1:47184948-47184957 chr1:47184511-47184520 chr1:47184509-47184521 chr1:47185021-47185030 chr1:47184880-47184894 chr1:47184947-47184959 chr1:47184947-47184959 chr1:47184949-47184958 chr1:47184948-47184958 chr1:47184918-47184927 chr1:47184510-47184519 chr1:47184948-47184958 chr1:47184822-47184843 chr1:47184948-47184962 chr1:47184898-47184905 chr1:47184948-47184957 chr1:47185078-47185088
28	GATA2	chr1:47184635-47185771	SH-SY5Y	brain:	n/a	chr1:47185457-47185471 chr1:47185619-47185626
29	POLR2A	chr1:47184073-47185283	GM12892	blood:	n/a	n/a
30	MAFK	chr1:47184991-47185337	K562	blood:	n/a	n/a
31	SP1	chr1:47184537-47185255	H1-hESC	embryonic stem cell:	n/a	chr1:47184883-47184894 chr1:47184948-47184957 chr1:47185021-47185030 chr1:47184880-47184894 chr1:47184947-47184959 chr1:47184947-47184959 chr1:47184949-47184958 chr1:47184948-47184958 chr1:47184918-47184927 chr1:47184948-47184958 chr1:47184822-47184843 chr1:47184948-47184962 chr1:47184898-47184905 chr1:47184948-47184957 chr1:47185078-47185088
32	POLR2A	chr1:47184227-47185263	GM18505	blood:	n/a	n/a
33	ELF1	chr1:47184237-47185229	K562	blood:	n/a	chr1:47184965-47184974 chr1:47184657-47184669 chr1:47184986-47184998
34	MYC	chr1:47184697-47185235	MCF10A-Er-Src	breast:	n/a	chr1:47185076-47185085
35	CHD2	chr1:47184514-47185705	Hela-S3	cervix:	n/a	n/a
36	MAX	chr1:47184540-47185321	NB4	blood:	n/a	chr1:47185076-47185085
37	JUND	chr1:47184429-47185417	SK-N-SH	brain:	n/a	chr1:47184831-47184840 chr1:47184852-47184861 chr1:47184512-47184521
38	CREB1	chr1:47184273-47185236	HepG2	liver:	n/a	chr1:47184850-47184863
39	SP1	chr1:47184319-47185840	HCT-116	colon:	n/a	chr1:47184883-47184894 chr1:47184509-47184521 chr1:47184948-47184957 chr1:47184511-47184520 chr1:47184509-47184521 chr1:47185021-47185030 chr1:47184880-47184894 chr1:47184947-47184959 chr1:47184947-47184959 chr1:47184949-47184958 chr1:47184948-47184958 chr1:47184918-47184927 chr1:47184510-47184519 chr1:47184948-47184958 chr1:47184822-47184843 chr1:47184948-47184962 chr1:47184898-47184905 chr1:47184948-47184957 chr1:47185078-47185088
40	POLR2A	chr1:47184240-47185239	GM12892	blood:	n/a	n/a
41	POLR2A	chr1:47184284-47185252	GM18951	blood:	n/a	n/a
42	MAZ	chr1:47184129-47185306	IMR90	lung:	n/a	chr1:47185076-47185085
43	POLR2A	chr1:47184447-47185256	HUVEC	blood vessel:	n/a	n/a
44	GABPA	chr1:47184638-47185261	MCF-7	breast:	n/a	chr1:47184949-47184958 chr1:47185020-47185029
45	CEBPD	chr1:47184325-47185795	K562	blood:	n/a	n/a
46	ZEB1	chr1:47184594-47185316	HepG2	liver:	n/a	n/a
47	POLR2A	chr1:47184071-47185321	GM12891	blood:	n/a	n/a
48	POLR2A	chr1:47184395-47185249	U87	brain:	n/a	n/a
49	POLR2A	chr1:47184389-47185249	U87	brain:	n/a	n/a
50	MYC	chr1:47184572-47185550	MCF10A-Er-Src	breast:	n/a	chr1:47185076-47185085

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:47185216-47185266	Jurkat	blood:	n/a
2	chr1:47185216-47185266	NH-A	brain:	n/a
3	chr1:47185216-47185266	HAEpiC	amniotic membrane:	n/a
4	chr1:47185216-47185266	ECC-1	luminal epithelium:	n/a
5	chr1:47185216-47185266	HRPEpiC	eye:	n/a
6	chr1:47185216-47185266	H1-hESC	embryonic stem cell:	embryo
7	chr1:47185216-47185266	Hepatocyte	liver:	n/a
8	chr1:47185216-47185266	HL-60	blood:	n/a
9	chr1:47185216-47185266	Caco-2	colon:	n/a
10	chr1:47185216-47185266	MCF-7	breast:	n/a
11	chr1:47185216-47185266	RPTEC	kidney:	n/a
12	chr1:47185216-47185266	HMEC	breast:	n/a
13	chr1:47185216-47185266	AG09309	skin:	n/a
14	chr1:47185216-47185266	HPAEpiC	pulmonary alveolar:	n/a
15	chr1:47185216-47185266	HNPCEpiC	eye:	n/a
16	chr1:47185216-47185266	GM12892	blood:	n/a
17	chr1:47185216-47185266	LNCaP	prostate:	n/a
18	chr1:47185216-47185266	PANC-1	pancreas:	n/a
19	chr1:47185216-47185266	HEEpiC	esophagus:	n/a
20	chr1:47185216-47185266	GM12878	blood:	n/a
21	chr1:47185216-47185266	K562	blood:	n/a
22	chr1:47185216-47185266	SK-N-MC	brain:	n/a
23	chr1:47185216-47185266	HUVEC	blood vessel:	n/a
24	chr1:47185216-47185266	NHBE	bronchial:	n/a
25	chr1:47185216-47185266	IMR90	lung:	fetal
26	chr1:47185216-47185266	HRCEpiC	kidney:	n/a
27	chr1:47185216-47185266	PFSK-1	brain:	n/a
28	chr1:47185216-47185266	HEK293	kidney:	embryo
29	chr1:47185216-47185266	AG04449	skin:	fetal
30	chr1:47185216-47185266	GM06990	blood:	n/a
31	chr1:47185216-47185266	PrEC	prostate:	n/a
32	chr1:47185216-47185266	AG04450	lung:	fetal
33	chr1:47185216-47185266	HIPEpiC	eye:	n/a
34	chr1:47185216-47185266	A549	lung:	n/a
35	chr1:47185216-47185266	AoSMC	blood vessel:	n/a
36	chr1:47185216-47185266	HCPEpiC	choroid plexus:	n/a
37	chr1:47185216-47185266	GM12891	blood:	n/a
38	chr1:47185216-47185266	AG09319	gingival:	n/a
39	chr1:47185216-47185266	SK-N-SH_RA	brain:	n/a
40	chr1:47185216-47185266	HepG2	liver:	n/a
41	chr1:47185216-47185266	NB4	blood:	n/a
42	chr1:47185216-47185266	SKMC	muscle:	n/a
43	chr1:47185216-47185266	Hela-S3	cervix:	n/a
44	chr1:47185216-47185266	ovcar-3	ovarian:	n/a
45	chr1:47185216-47185266	CMK	blood:	n/a
46	chr1:47185216-47185266	T-47D	breast:	n/a
47	chr1:47185216-47185266	NT2-D1	testis:	n/a
48	chr1:47185216-47185266	NHDF-neo	bronchial:	n/a
49	chr1:47185216-47185266	GM19239	blood:	n/a
50	chr1:47185216-47185266	BE2_C	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:47134358..47137339-chr1:47183387..47185827,2	MCF-7	breast:
2	chr1:47133847..47136859-chr1:47183270..47186412,3	K562	blood:
3	chr1:47080724..47082396-chr1:47183672..47185631,2	MCF-7	breast:
4	chr1:47132021..47134292-chr1:47182751..47186267,3	MCF-7	breast:
5	chr1:46871688..46875401-chr1:47182655..47185240,3	K562	blood:
6	chr1:47131887..47139340-chr1:47181784..47186573,11	K562	blood:

Variant related genes	Relation type
EFCAB14	TF binding region
EFCAB14	CpG island
ENSG00000186118	Chromatin interaction
ENSG00000233647	Chromatin interaction
ENSG00000117480	Chromatin interaction
ENSG00000142961	Chromatin interaction
ENSG00000123472	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1258062	1.00[AMR][1000 genomes]
rs17102443	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17102459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2984805	1.00[AMR][1000 genomes]
rs58568840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs599869	1.00[AMR][1000 genomes]
rs635972	1.00[AMR][1000 genomes]
rs644675	1.00[AMR][1000 genomes]
rs654509	1.00[AMR][1000 genomes]
rs659308	1.00[AMR][1000 genomes]
rs682000	1.00[AMR][1000 genomes]
rs72886508	1.00[AMR][1000 genomes]
rs72886510	1.00[AMR][1000 genomes]
rs72886514	1.00[AMR][1000 genomes]
rs72898800	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72900717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72900756	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72900763	1.00[AMR][1000 genomes]
rs72900764	1.00[AMR][1000 genomes]
rs72900776	1.00[AMR][1000 genomes]
rs7544284	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47183400-47185400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:47183800-47185400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr1:47183800-47185400	Active TSS	Aorta	Aorta
4	chr1:47183800-47185400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:47184000-47185400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr1:47184000-47185400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:47184000-47185400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:47184000-47185400	Active TSS	Brain Germinal Matrix	brain
9	chr1:47184000-47185400	Active TSS	Esophagus	oesophagus
10	chr1:47184000-47185400	Active TSS	Ovary	ovary
11	chr1:47184000-47185400	Active TSS	Right Atrium	heart
12	chr1:47184000-47185400	Active TSS	Stomach Mucosa	stomach
13	chr1:47184000-47185600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:47184000-47185600	Active TSS	Psoas Muscle	Psoas
15	chr1:47184000-47185800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:47184000-47185800	Active TSS	Lung	lung
17	chr1:47184200-47185400	Active TSS	H1 Cell Line	embryonic stem cell
18	chr1:47184200-47185400	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr1:47184200-47185400	Active TSS	Fetal Muscle Trunk	muscle
20	chr1:47184200-47185400	Active TSS	Right Ventricle	heart
21	chr1:47184200-47185400	Active TSS	Stomach Smooth Muscle	stomach
22	chr1:47184200-47185400	Active TSS	HSMMtube	muscle
23	chr1:47184200-47185600	Active TSS	Muscle Satellite Cultured Cells	--
24	chr1:47184200-47185600	Active TSS	Fetal Muscle Leg	muscle
25	chr1:47184800-47185400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:47184800-47185400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:47185000-47185400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr1:47185000-47185400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
29	chr1:47185000-47185400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:47185000-47185400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr1:47185000-47185400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr1:47185000-47185400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:47185000-47185400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:47185000-47185400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr1:47185000-47185400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:47185000-47185400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:47185000-47185400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:47185000-47185400	Flanking Active TSS	Liver	Liver
39	chr1:47185000-47185400	Flanking Active TSS	Placenta	Placenta
40	chr1:47185000-47185400	Flanking Active TSS	Fetal Thymus	thymus
41	chr1:47185000-47185400	Flanking Active TSS	HMEC	breast
42	chr1:47185000-47185400	Flanking Active TSS	NH-A	brain
43	chr1:47185000-47185600	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr1:47185000-47185600	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr1:47185000-47185600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr1:47185000-47185600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:47185000-47185600	Weak transcription	Small Intestine	intestine
48	chr1:47185000-47185600	Flanking Active TSS	NHEK	skin
49	chr1:47185000-47185800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:47185000-47185800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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