Variant report

Variant	rs72896513
Chromosome Location	chr1:47656018-47656019
allele	A/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	STAT3	chr1:47655666-47656355	MCF10A-Er-Src	breast:	n/a	chr1:47655955-47655966 chr1:47656035-47656046
2	STAT3	chr1:47655686-47656321	MCF10A-Er-Src	breast:	n/a	chr1:47655955-47655966 chr1:47656035-47656046
3	MYC	chr1:47655703-47656315	MCF10A-Er-Src	breast:	n/a	chr1:47656026-47656036
4	STAT3	chr1:47655671-47656257	MCF10A-Er-Src	breast:	n/a	chr1:47655955-47655966 chr1:47656035-47656046
5	POLR2A	chr1:47655850-47656351	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:47655501-47656322	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr1:47655685-47656352	MCF10A-Er-Src	breast:	n/a	n/a
8	E2F6	chr1:47655570-47656117	A549	lung:	n/a	n/a
9	CEBPB	chr1:47655906-47656192	A549	lung:	n/a	chr1:47656057-47656070
10	MYC	chr1:47655625-47656380	MCF10A-Er-Src	breast:	n/a	chr1:47656026-47656036
11	SP1	chr1:47655666-47656127	A549	lung:	n/a	chr1:47656026-47656036 chr1:47656025-47656037 chr1:47656026-47656036 chr1:47656026-47656035 chr1:47656025-47656037 chr1:47656027-47656036
12	RCOR1	chr1:47655865-47656187	Hela-S3	cervix:	n/a	n/a
13	STAT3	chr1:47655758-47656263	MCF10A-Er-Src	breast:	n/a	chr1:47655955-47655966 chr1:47656035-47656046
14	E2F4	chr1:47655776-47656279	MCF10A-Er-Src	breast:	n/a	chr1:47656177-47656192
15	E2F6	chr1:47655501-47656443	A549	lung:	n/a	chr1:47656177-47656192
16	MAX	chr1:47655766-47656364	Hela-S3	cervix:	n/a	chr1:47656026-47656036
17	FOS	chr1:47655683-47656262	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr1:47655859-47656283	Hela-S3	cervix:	n/a	n/a
19	SMARCB1	chr1:47655466-47656552	Hela-S3	cervix:	n/a	n/a
20	FOS	chr1:47655745-47656180	MCF10A-Er-Src	breast:	n/a	n/a
21	MAX	chr1:47655523-47656361	A549	lung:	n/a	chr1:47656026-47656036
22	MAZ	chr1:47655925-47656224	K562	blood:	n/a	chr1:47656026-47656036
23	MAX	chr1:47655783-47656203	A549	lung:	n/a	chr1:47656026-47656036
24	SMC3	chr1:47655922-47656169	Hela-S3	cervix:	n/a	n/a
25	JUND	chr1:47655871-47656150	K562	blood:	n/a	n/a
26	RCOR1	chr1:47655684-47656375	IMR90	lung:	n/a	n/a
27	FOS	chr1:47655704-47656208	MCF10A-Er-Src	breast:	n/a	n/a
28	MAZ	chr1:47655585-47656475	IMR90	lung:	n/a	chr1:47656026-47656036
29	MAX	chr1:47655403-47656532	A549	lung:	n/a	chr1:47656026-47656036
30	POLR2A	chr1:47655407-47656357	MCF10A-Er-Src	breast:	n/a	n/a
31	CEBPB	chr1:47655888-47656231	IMR90	lung:	n/a	chr1:47656057-47656070
32	CEBPB	chr1:47655881-47656233	Hela-S3	cervix:	n/a	chr1:47656057-47656070
33	POLR2A	chr1:47655874-47656267	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:47656003-47656053	IMR90	lung:	fetal
2	chr1:47656003-47656053	AG04449	skin:	fetal
3	chr1:47656003-47656053	HNPCEpiC	eye:	n/a
4	chr1:47656003-47656053	AG04450	lung:	fetal
5	chr1:47656003-47656053	GM12891	blood:	n/a
6	chr1:47656003-47656053	T-47D	breast:	n/a
7	chr1:47656003-47656053	SKMC	muscle:	n/a
8	chr1:47656003-47656053	HIPEpiC	eye:	n/a
9	chr1:47656003-47656053	H1-hESC	embryonic stem cell:	embryo
10	chr1:47656003-47656053	PANC-1	pancreas:	n/a
11	chr1:47656003-47656053	HCM	heart:	n/a
12	chr1:47656003-47656053	HCF	heart:	n/a
13	chr1:47656003-47656053	LNCaP	prostate:	n/a
14	chr1:47656003-47656053	HL-60	blood:	n/a
15	chr1:47656003-47656053	GM12892	blood:	n/a
16	chr1:47656003-47656053	MCF-7	breast:	n/a
17	chr1:47656003-47656053	U87	brain:	n/a
18	chr1:47656003-47656053	NT2-D1	testis:	n/a
19	chr1:47656003-47656053	GM12878	blood:	n/a
20	chr1:47656003-47656053	AoSMC	blood vessel:	n/a
21	chr1:47656003-47656053	AG09309	skin:	n/a
22	chr1:47656003-47656053	HRCEpiC	kidney:	n/a
23	chr1:47656003-47656053	PrEC	prostate:	n/a
24	chr1:47656003-47656053	BE2_C	brain:	n/a
25	chr1:47656003-47656053	HepG2	liver:	n/a
26	chr1:47656003-47656053	ProgFib	skin:	n/a
27	chr1:47656003-47656053	HEEpiC	esophagus:	n/a
28	chr1:47656003-47656053	SK-N-MC	brain:	n/a
29	chr1:47656003-47656053	MCF10A-Er-Src	breast:	n/a
30	chr1:47656003-47656053	AG09319	gingival:	n/a
31	chr1:47656003-47656053	SAEC	small airway:	n/a
32	chr1:47656003-47656053	A549	lung:	n/a
33	chr1:47656003-47656053	CMK	blood:	n/a
34	chr1:47656003-47656053	HMEC	breast:	n/a
35	chr1:47656003-47656053	AG10803	skin:	n/a
36	chr1:47656003-47656053	HAEpiC	amniotic membrane:	n/a
37	chr1:47656003-47656053	HCPEpiC	choroid plexus:	n/a
38	chr1:47656003-47656053	SK-N-SH	brain:	n/a
39	chr1:47656003-47656053	NH-A	brain:	n/a
40	chr1:47656003-47656053	HCT-116	colon:	n/a
41	chr1:47656003-47656053	GM19239	blood:	n/a
42	chr1:47656003-47656053	HRE	kidney:	n/a
43	chr1:47656003-47656053	Hepatocyte	liver:	n/a
44	chr1:47656003-47656053	HEK293	kidney:	embryo
45	chr1:47656003-47656053	RPTEC	kidney:	n/a
46	chr1:47656003-47656053	ECC-1	luminal epithelium:	n/a
47	chr1:47656003-47656053	BJ	skin:	n/a
48	chr1:47656003-47656053	ovcar-3	ovarian:	n/a
49	chr1:47656003-47656053	HPAEpiC	pulmonary alveolar:	n/a
50	chr1:47656003-47656053	Caco-2	colon:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47655819..47657436-chr1:47799137..47801227,2	K562	blood:

Variant related genes	Relation type
PDZK1IP1	TF binding region
PDZK1IP1	CpG island
ENSG00000162368	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11211493	1.00[AMR][1000 genomes]
rs11211518	1.00[AMR][1000 genomes]
rs12057442	1.00[AMR][1000 genomes]
rs12061831	1.00[AMR][1000 genomes]
rs12094830	1.00[AMR][1000 genomes]
rs12097707	1.00[AMR][1000 genomes]
rs2088998	1.00[AMR][1000 genomes]
rs58846358	1.00[AMR][1000 genomes]
rs58921777	1.00[AMR][1000 genomes]
rs59984926	1.00[AMR][1000 genomes]
rs6682932	1.00[AMR][1000 genomes]
rs72892699	1.00[AMR][1000 genomes]
rs72894542	1.00[AMR][1000 genomes]
rs72894554	1.00[AMR][1000 genomes]
rs72894556	1.00[AMR][1000 genomes]
rs72894561	1.00[AMR][1000 genomes]
rs72894566	1.00[AMR][1000 genomes]
rs72894577	1.00[AMR][1000 genomes]
rs72896510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7545862	1.00[AMR][1000 genomes]
rs8034132	1.00[AMR][1000 genomes]
rs9436428	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916813	chr1:47435635-47666179	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47652600-47659000	Enhancers	Fetal Intestine Small	intestine
2	chr1:47652800-47658400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:47653200-47658400	Enhancers	K562	blood
4	chr1:47653600-47656600	Enhancers	HepG2	liver
5	chr1:47654600-47659200	Enhancers	Fetal Intestine Large	intestine
6	chr1:47655000-47656400	Flanking Active TSS	Pancreas	Pancrea
7	chr1:47655000-47656600	Enhancers	A549	lung
8	chr1:47655000-47659000	Enhancers	Lung	lung
9	chr1:47655000-47659200	Enhancers	Fetal Muscle Leg	muscle
10	chr1:47655200-47656400	Enhancers	Right Atrium	heart
11	chr1:47655200-47658400	Enhancers	Fetal Muscle Trunk	muscle
12	chr1:47655200-47659000	Enhancers	Adipose Nuclei	Adipose
13	chr1:47655400-47656200	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr1:47655400-47656200	Enhancers	Hela-S3	cervix
15	chr1:47655400-47656600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:47655400-47657200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:47655400-47658200	Enhancers	HMEC	breast
18	chr1:47655400-47658800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:47655400-47659400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:47655600-47656200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:47655600-47656600	Enhancers	H1 Cell Line	embryonic stem cell
22	chr1:47655600-47656600	Bivalent Enhancer	Fetal Stomach	stomach
23	chr1:47655600-47656600	Enhancers	Ovary	ovary
24	chr1:47655600-47656600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr1:47655600-47656800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:47655600-47657000	Enhancers	Right Ventricle	heart
27	chr1:47655600-47657400	Enhancers	Spleen	Spleen
28	chr1:47655600-47657800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:47655600-47657800	Weak transcription	Small Intestine	intestine
30	chr1:47655600-47658600	Enhancers	NHEK	skin
31	chr1:47655600-47659000	Enhancers	Placenta	Placenta
32	chr1:47655600-47659000	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr1:47655600-47659000	Enhancers	HSMMtube	muscle
34	chr1:47655600-47659200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr1:47655800-47656400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:47655800-47656400	Enhancers	Fetal Lung	lung
37	chr1:47655800-47656400	Enhancers	Rectal Smooth Muscle	rectum
38	chr1:47655800-47656400	Enhancers	NH-A	brain
39	chr1:47655800-47656600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
40	chr1:47655800-47656600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:47655800-47656600	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr1:47655800-47656600	Enhancers	Brain Hippocampus Middle	brain
43	chr1:47655800-47656800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
44	chr1:47655800-47656800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr1:47655800-47656800	Enhancers	HSMM	muscle
46	chr1:47655800-47657000	Enhancers	HUVEC	blood vessel
47	chr1:47655800-47657600	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr1:47655800-47657800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:47655800-47658000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:47655800-47658000	Enhancers	NHDF-Ad	bronchial

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