Variant report

Variant	rs72936680
Chromosome Location	chr3:98620679-98620680
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	RELA	chr3:98620286-98621055	GM15510	blood:	n/a	n/a
2	E2F4	chr3:98620041-98621122	MCF10A-Er-Src	breast:	n/a	n/a
3	SMC3	chr3:98620659-98621254	Hela-S3	cervix:	n/a	n/a
4	TAF1	chr3:98620116-98621139	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr3:98620089-98621148	HUVEC	blood vessel:	n/a	n/a
6	TAF1	chr3:98619761-98621074	SK-N-SH	brain:	n/a	n/a
7	MAZ	chr3:98619241-98621681	IMR90	lung:	n/a	n/a
8	HA-E2F1	chr3:98619996-98621050	Hela-S3	cervix:	n/a	n/a
9	NRF1	chr3:98620419-98620794	GM12878	blood:	n/a	n/a
10	IRF1	chr3:98620319-98621133	K562	blood:	n/a	chr3:98620770-98620784 chr3:98620574-98620588
11	CHD2	chr3:98620168-98621338	HepG2	liver:	n/a	chr3:98620361-98620371
12	GABPA	chr3:98620509-98621310	MCF-7	breast:	n/a	n/a
13	ZBTB7A	chr3:98619646-98621127	ECC-1	luminal epithelium:	n/a	chr3:98620704-98620711
14	REST	chr3:98620339-98620711	PANC-1	pancreas:	n/a	chr3:98620358-98620368
15	EP300	chr3:98619783-98621301	SK-N-SH	brain:	n/a	chr3:98620499-98620515 chr3:98620885-98620892 chr3:98621042-98621056
16	ELF1	chr3:98620615-98621080	K562	blood:	n/a	chr3:98620858-98620870 chr3:98620884-98620895 chr3:98620885-98620894 chr3:98620883-98620896
17	MAX	chr3:98619724-98621179	HepG2	liver:	n/a	n/a
18	POLR2A	chr3:98620258-98621168	PANC-1	pancreas:	n/a	n/a
19	REST	chr3:98619564-98621432	H1-neurons	neurons:	n/a	chr3:98620358-98620368
20	SIN3A	chr3:98620540-98620872	GM12878	blood:	n/a	n/a
21	TAF1	chr3:98619078-98621229	A549	lung:	n/a	n/a
22	JUN	chr3:98620422-98620990	K562	blood:	n/a	n/a
23	SP4	chr3:98620276-98621002	H1-hESC	embryonic stem cell:	n/a	chr3:98620574-98620590 chr3:98620772-98620783 chr3:98620576-98620592
24	JUND	chr3:98620031-98621069	K562	blood:	n/a	n/a
25	E2F4	chr3:98620530-98620725	GM12878	blood:	n/a	n/a
26	MAX	chr3:98619785-98621388	MCF-7	breast:	n/a	n/a
27	MXI1	chr3:98619865-98620887	H1-hESC	embryonic stem cell:	n/a	n/a
28	STAT3	chr3:98620650-98620799	MCF10A-Er-Src	breast:	n/a	n/a
29	E2F6	chr3:98620149-98621214	H1-hESC	embryonic stem cell:	n/a	n/a
30	GABPA	chr3:98620576-98621029	K562	blood:	n/a	n/a
31	POLR2A	chr3:98619780-98621155	H1-hESC	embryonic stem cell:	n/a	n/a
32	UBTF	chr3:98619691-98621034	K562	blood:	n/a	n/a
33	UBTF	chr3:98619758-98621017	K562	blood:	n/a	n/a
34	POLR2A	chr3:98620223-98621195	SK-N-MC	brain:	n/a	n/a
35	ARID3A	chr3:98620387-98621035	HepG2	liver:	n/a	n/a
36	SP1	chr3:98620453-98621151	H1-hESC	embryonic stem cell:	n/a	chr3:98620772-98620783 chr3:98620982-98620996 chr3:98620576-98620588 chr3:98620772-98620784 chr3:98620577-98620587 chr3:98620576-98620588 chr3:98620773-98620787 chr3:98620772-98620784 chr3:98620577-98620587
37	GATA2	chr3:98619874-98621719	SH-SY5Y	brain:	n/a	chr3:98621157-98621168
38	BHLHE40	chr3:98620008-98621079	K562	blood:	n/a	chr3:98620210-98620226 chr3:98620251-98620267
39	POLR2A	chr3:98619866-98621061	HUVEC	blood vessel:	n/a	n/a
40	RCOR1	chr3:98619861-98621540	K562	blood:	n/a	n/a
41	SP2	chr3:98620472-98620886	K562	blood:	n/a	chr3:98620699-98620714 chr3:98620702-98620711
42	REST	chr3:98619641-98621253	A549	lung:	n/a	chr3:98620358-98620368
43	YY1	chr3:98619985-98621054	GM12892	blood:	n/a	chr3:98620437-98620446 chr3:98620255-98620266 chr3:98620858-98620872 chr3:98620208-98620219
44	HA-E2F1	chr3:98619690-98621251	MCF-7	breast:	n/a	chr3:98619867-98619876
45	POLR2A	chr3:98619772-98621198	GM12892	blood:	n/a	n/a
46	POLR2A	chr3:98620283-98621046	HepG2	liver:	n/a	n/a
47	TAF1	chr3:98619982-98621010	HepG2	liver:	n/a	n/a
48	PAX5	chr3:98620315-98620784	GM12878	blood:	n/a	n/a
49	SP1	chr3:98619263-98621521	HCT-116	colon:	n/a	chr3:98620772-98620783 chr3:98620982-98620996 chr3:98621186-98621196 chr3:98620576-98620588 chr3:98620772-98620784 chr3:98621186-98621195 chr3:98620577-98620587 chr3:98621182-98621196 chr3:98620576-98620588 chr3:98620773-98620787 chr3:98620392-98620401 chr3:98620772-98620784 chr3:98620577-98620587
50	MXI1	chr3:98620432-98621128	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:98620662-98620712	HRE	kidney:	n/a
2	chr3:98620635-98620685	HIPEpiC	eye:	n/a
3	chr3:98620662-98620712	HIPEpiC	eye:	n/a
4	chr3:98620662-98620712	AG09309	skin:	n/a
5	chr3:98620635-98620685	ProgFib	skin:	n/a
6	chr3:98620662-98620712	HCM	heart:	n/a
7	chr3:98620662-98620712	A549	lung:	n/a
8	chr3:98620635-98620685	SKMC	muscle:	n/a
9	chr3:98620662-98620712	RPTEC	kidney:	n/a
10	chr3:98620662-98620712	HUVEC	blood vessel:	n/a
11	chr3:98620662-98620712	MCF10A-Er-Src	breast:	n/a
12	chr3:98620635-98620685	H1-hESC	embryonic stem cell:	embryo
13	chr3:98620662-98620712	CMK	blood:	n/a
14	chr3:98620635-98620685	PANC-1	pancreas:	n/a
15	chr3:98620662-98620712	IMR90	lung:	fetal
16	chr3:98620635-98620685	HepG2	liver:	n/a
17	chr3:98620662-98620712	ECC-1	luminal epithelium:	n/a
18	chr3:98620662-98620712	MCF-7	breast:	n/a
19	chr3:98620662-98620712	NHDF-neo	bronchial:	n/a
20	chr3:98620635-98620685	NH-A	brain:	n/a
21	chr3:98620662-98620712	HCPEpiC	choroid plexus:	n/a
22	chr3:98620635-98620685	A549	lung:	n/a
23	chr3:98620662-98620712	PFSK-1	brain:	n/a
24	chr3:98620662-98620712	HEK293	kidney:	embryo
25	chr3:98620662-98620712	T-47D	breast:	n/a
26	chr3:98620635-98620685	MCF-7	breast:	n/a
27	chr3:98620635-98620685	HL-60	blood:	n/a
28	chr3:98620635-98620685	HCPEpiC	choroid plexus:	n/a
29	chr3:98620635-98620685	AG09309	skin:	n/a
30	chr3:98620662-98620712	SK-N-SH	brain:	n/a
31	chr3:98620635-98620685	HAEpiC	amniotic membrane:	n/a
32	chr3:98620635-98620685	HNPCEpiC	eye:	n/a
33	chr3:98620662-98620712	GM12891	blood:	n/a
34	chr3:98620635-98620685	HRCEpiC	kidney:	n/a
35	chr3:98620662-98620712	HPAEpiC	pulmonary alveolar:	n/a
36	chr3:98620635-98620685	U87	brain:	n/a
37	chr3:98620635-98620685	ECC-1	luminal epithelium:	n/a
38	chr3:98620635-98620685	HEEpiC	esophagus:	n/a
39	chr3:98620635-98620685	GM12891	blood:	n/a
40	chr3:98620662-98620712	HAEpiC	amniotic membrane:	n/a
41	chr3:98620635-98620685	NB4	blood:	n/a
42	chr3:98620662-98620712	H1-hESC	embryonic stem cell:	embryo
43	chr3:98620635-98620685	HEK293	kidney:	embryo
44	chr3:98620662-98620712	HEEpiC	esophagus:	n/a
45	chr3:98620662-98620712	LNCaP	prostate:	n/a
46	chr3:98620662-98620712	HL-60	blood:	n/a
47	chr3:98620662-98620712	U87	brain:	n/a
48	chr3:98620662-98620712	HMEC	breast:	n/a
49	chr3:98620662-98620712	GM19239	blood:	n/a
50	chr3:98620662-98620712	NH-A	brain:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98620298..98622928-chr3:98626076..98627807,2	MCF-7	breast:
2	chr15:65596821..65597625-chr3:98620042..98620956,2	HCT-116	colon:

Variant related genes	Relation type
DCBLD2	TF binding region
ENSG00000239462	TF binding region
ENSG00000239462	CpG island
DCBLD2	CpG island
ENSG00000207331	Chromatin interaction
ENSG00000200156	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs57266345	0.87[AFR][1000 genomes]
rs57962467	1.00[AMR][1000 genomes]
rs59684850	0.82[AFR][1000 genomes]
rs61228839	0.95[AFR][1000 genomes]
rs72930963	0.82[AFR][1000 genomes]
rs72930970	0.82[AFR][1000 genomes]
rs72934618	0.87[AFR][1000 genomes]
rs72934634	0.83[AFR][1000 genomes]
rs72936606	0.87[AFR][1000 genomes]
rs72936636	0.95[AFR][1000 genomes]
rs72936671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938508	0.95[AFR][1000 genomes]
rs72938510	0.95[AFR][1000 genomes]
rs72938569	0.95[AFR][1000 genomes]
rs72940503	0.95[AFR][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	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98615600-98621200	Active TSS	NHLF	lung
2	chr3:98616600-98621400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:98616800-98621200	Active TSS	NHDF-Ad	bronchial
4	chr3:98617400-98621200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:98617400-98622000	Active TSS	Right Ventricle	heart
6	chr3:98617600-98621200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr3:98618200-98621800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr3:98618400-98621200	Active TSS	H1 Cell Line	embryonic stem cell
9	chr3:98618400-98621200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr3:98618400-98621200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:98618400-98621200	Active TSS	Fetal Kidney	kidney
12	chr3:98618400-98621200	Active TSS	GM12878-XiMat	blood
13	chr3:98618400-98621400	Active TSS	Left Ventricle	heart
14	chr3:98618400-98621600	Active TSS	Right Atrium	heart
15	chr3:98618400-98621800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:98618600-98621200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:98618600-98621400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:98618600-98621600	Active TSS	Ovary	ovary
19	chr3:98618600-98621800	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr3:98618600-98621800	Active TSS	HSMMtube	muscle
21	chr3:98618800-98621200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:98618800-98621200	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr3:98618800-98621200	Active TSS	Stomach Smooth Muscle	stomach
24	chr3:98618800-98621400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:98618800-98621600	Active TSS	Psoas Muscle	Psoas
26	chr3:98618800-98621800	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr3:98618800-98622200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:98619000-98621200	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr3:98619000-98621200	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr3:98619000-98621200	Active TSS	HSMM	muscle
31	chr3:98619000-98621600	Active TSS	Fetal Muscle Trunk	muscle
32	chr3:98619200-98620800	Active TSS	HepG2	liver
33	chr3:98619200-98621200	Active TSS	Brain Substantia Nigra	brain
34	chr3:98619200-98621200	Active TSS	HMEC	breast
35	chr3:98619200-98621200	Active TSS	K562	blood
36	chr3:98619200-98621400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr3:98619200-98621600	Active TSS	H9 Cell Line	embryonic stem cell
38	chr3:98619200-98621600	Active TSS	Aorta	Aorta
39	chr3:98619400-98621000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:98619400-98621200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:98619400-98621200	Active TSS	Fetal Lung	lung
42	chr3:98619400-98621200	Active TSS	Lung	lung
43	chr3:98619400-98621200	Active TSS	A549	lung
44	chr3:98619400-98621400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:98619400-98621400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:98619400-98621400	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr3:98619400-98621600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:98619600-98620800	Active TSS	Fetal Brain Male	brain
49	chr3:98619600-98621000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:98619600-98621000	Active TSS	HUVEC	blood vessel

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