Variant report

Variant	rs564394806
Chromosome Location	chr3:24536883-24536884
allele	G/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	CTCF	chr3:24535467-24537699	A549	lung:	n/a	chr3:24536750-24536759 chr3:24535554-24535567 chr3:24536379-24536392 chr3:24536385-24536398
2	CEBPD	chr3:24536732-24537425	K562	blood:	n/a	n/a
3	YY1	chr3:24536080-24536970	H1-hESC	embryonic stem cell:	n/a	chr3:24536946-24536960 chr3:24536717-24536726 chr3:24536791-24536805 chr3:24536793-24536804 chr3:24536394-24536403 chr3:24536790-24536799 chr3:24536796-24536805 chr3:24536790-24536801 chr3:24536720-24536729 chr3:24536793-24536802 chr3:24536406-24536420 chr3:24536794-24536808
4	ELF1	chr3:24536469-24537407	K562	blood:	n/a	chr3:24536712-24536724 chr3:24536792-24536804 chr3:24536793-24536802 chr3:24536796-24536805 chr3:24536717-24536726 chr3:24536948-24536960
5	POLR2A	chr3:24536732-24537296	H1-hESC	embryonic stem cell:	n/a	n/a
6	ZBTB7A	chr3:24535385-24537221	K562	blood:	n/a	n/a
7	HA-E2F1	chr3:24535299-24537654	MCF-7	breast:	n/a	chr3:24536718-24536728 chr3:24536394-24536403 chr3:24537395-24537404 chr3:24536790-24536799 chr3:24536794-24536804 chr3:24536392-24536402 chr3:24536791-24536801 chr3:24536633-24536643 chr3:24537090-24537107
8	CREB1	chr3:24536810-24537255	A549	lung:	n/a	n/a
9	HEY1	chr3:24535449-24537529	K562	blood:	n/a	chr3:24536750-24536765 chr3:24536479-24536494 chr3:24536491-24536506 chr3:24536707-24536722 chr3:24536792-24536807
10	ZEB1	chr3:24535519-24537509	HepG2	liver:	n/a	chr3:24536969-24536980
11	CREB1	chr3:24535582-24537508	K562	blood:	n/a	n/a
12	POLR2A	chr3:24536881-24537438	HepG2	liver:	n/a	n/a
13	EGR1	chr3:24536808-24537186	MCF-7	breast:	n/a	chr3:24536950-24536963 chr3:24536950-24536963 chr3:24536951-24536962 chr3:24537044-24537054 chr3:24536951-24536961 chr3:24536950-24536963
14	EGR1	chr3:24535548-24537617	HCT-116	colon:	n/a	chr3:24536378-24536391 chr3:24536007-24536017 chr3:24536005-24536019 chr3:24536379-24536389 chr3:24536377-24536392 chr3:24537391-24537400 chr3:24536950-24536963 chr3:24536007-24536017 chr3:24536950-24536963 chr3:24536122-24536135 chr3:24536007-24536018 chr3:24537396-24537409 chr3:24536378-24536391 chr3:24536372-24536385 chr3:24536951-24536962 chr3:24537044-24537054 chr3:24536007-24536016 chr3:24536951-24536961 chr3:24536122-24536132 chr3:24536006-24536019 chr3:24536950-24536963 chr3:24537394-24537404 chr3:24537396-24537406
15	MAX	chr3:24535349-24537594	K562	blood:	n/a	chr3:24536125-24536135 chr3:24537396-24537406 chr3:24536847-24536857 chr3:24536381-24536391 chr3:24536143-24536153
16	PML	chr3:24536548-24537517	K562	blood:	n/a	n/a
17	MXI1	chr3:24535442-24537411	HepG2	liver:	n/a	n/a
18	POLR2A	chr3:24535466-24537678	K562	blood:	n/a	n/a
19	CBX3	chr3:24536803-24537440	K562	blood:	n/a	n/a
20	NR2F2	chr3:24536111-24537511	K562	blood:	n/a	n/a
21	TAF1	chr3:24536073-24537496	K562	blood:	n/a	n/a
22	EP300	chr3:24535384-24537629	ECC-1	luminal epithelium:	n/a	chr3:24536788-24536804 chr3:24536792-24536808 chr3:24536879-24536895 chr3:24536719-24536728 chr3:24536794-24536803 chr3:24536386-24536402
23	HA-E2F1	chr3:24535794-24537412	Hela-S3	cervix:	n/a	chr3:24536718-24536728 chr3:24536394-24536403 chr3:24537395-24537404 chr3:24536790-24536799 chr3:24536794-24536804 chr3:24536392-24536402 chr3:24536791-24536801 chr3:24536633-24536643 chr3:24537090-24537107
24	MAZ	chr3:24535500-24537843	HepG2	liver:	n/a	chr3:24536125-24536135 chr3:24537396-24537406 chr3:24536847-24536857 chr3:24536381-24536391 chr3:24536143-24536153
25	POLR2A	chr3:24535758-24537506	K562	blood:	n/a	n/a
26	TAF7	chr3:24536807-24537427	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr3:24536556-24537340	K562	blood:	n/a	chr3:24536750-24536759
28	BCLAF1	chr3:24536390-24537434	K562	blood:	n/a	chr3:24537233-24537242 chr3:24536822-24536835 chr3:24536795-24536804 chr3:24536942-24536955 chr3:24536885-24536893 chr3:24536610-24536618 chr3:24536792-24536801 chr3:24536796-24536809 chr3:24537394-24537403 chr3:24536718-24536727 chr3:24536792-24536805
29	RAD21	chr3:24536452-24536976	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr3:24535656-24537640	HCT-116	colon:	n/a	chr3:24536125-24536135 chr3:24537396-24537406 chr3:24536847-24536857 chr3:24536381-24536391 chr3:24536143-24536153
31	ZNF384	chr3:24536714-24537399	K562	blood:	n/a	n/a
32	ETS1	chr3:24536450-24537481	K562	blood:	n/a	chr3:24536715-24536726 chr3:24537395-24537406 chr3:24536796-24536807 chr3:24536491-24536504 chr3:24536790-24536801 chr3:24536793-24536804
33	POLR2A	chr3:24535405-24537667	HepG2	liver:	n/a	n/a
34	SMARCB1	chr3:24535448-24537477	Hela-S3	cervix:	n/a	n/a
35	TEAD4	chr3:24536807-24537544	K562	blood:	n/a	n/a
36	CTCF	chr3:24536542-24536997	K562	blood:	n/a	chr3:24536750-24536759
37	E2F6	chr3:24535505-24537406	K562	blood:	n/a	chr3:24536718-24536728 chr3:24536394-24536403 chr3:24537395-24537404 chr3:24536790-24536799 chr3:24536794-24536804 chr3:24536392-24536402 chr3:24536791-24536801 chr3:24536633-24536643 chr3:24537090-24537107
38	BCLAF1	chr3:24536806-24537369	K562	blood:	n/a	chr3:24537233-24537242 chr3:24536822-24536835 chr3:24536942-24536955 chr3:24536885-24536893
39	MAX	chr3:24535393-24537604	ECC-1	luminal epithelium:	n/a	chr3:24536125-24536135 chr3:24537396-24537406 chr3:24536847-24536857 chr3:24536381-24536391 chr3:24536143-24536153
40	BHLHE40	chr3:24535577-24537465	K562	blood:	n/a	chr3:24536711-24536727 chr3:24536474-24536490 chr3:24536784-24536800
41	EGR1	chr3:24536684-24537254	ECC-1	luminal epithelium:	n/a	chr3:24536950-24536963 chr3:24536950-24536963 chr3:24536951-24536962 chr3:24537044-24537054 chr3:24536951-24536961 chr3:24536950-24536963
42	SMARCC1	chr3:24535422-24537518	Hela-S3	cervix:	n/a	n/a
43	TAL1	chr3:24535417-24537447	K562	blood:	n/a	chr3:24537308-24537323 chr3:24537308-24537323 chr3:24537308-24537323 chr3:24537309-24537320
44	TAF1	chr3:24536788-24537629	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr3:24536532-24537381	A549	lung:	n/a	n/a
46	POLR2A	chr3:24535504-24537653	K562	blood:	n/a	n/a
47	E2F4	chr3:24535387-24537486	K562	blood:	n/a	chr3:24536718-24536728 chr3:24536394-24536403 chr3:24537395-24537404 chr3:24536790-24536799 chr3:24536794-24536804 chr3:24536392-24536402 chr3:24536791-24536801 chr3:24536633-24536643 chr3:24537090-24537107
48	POLR2A	chr3:24535410-24537534	K562	blood:	n/a	n/a
49	TAF1	chr3:24535584-24536950	K562	blood:	n/a	n/a
50	POLR2A	chr3:24536769-24537434	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:24536880-24536930	Jurkat	blood:	n/a
2	chr3:24536880-24536930	PANC-1	pancreas:	n/a
3	chr3:24536880-24536930	Hepatocyte	liver:	n/a
4	chr3:24536880-24536930	HPAEpiC	pulmonary alveolar:	n/a
5	chr3:24536880-24536930	SK-N-MC	brain:	n/a
6	chr3:24536880-24536930	ovcar-3	ovarian:	n/a
7	chr3:24536880-24536930	BJ	skin:	n/a
8	chr3:24536880-24536930	K562	blood:	n/a
9	chr3:24536880-24536930	HCPEpiC	choroid plexus:	n/a
10	chr3:24536880-24536930	SK-N-SH_RA	brain:	n/a
11	chr3:24536880-24536930	H1-hESC	embryonic stem cell:	embryo
12	chr3:24536880-24536930	HepG2	liver:	n/a
13	chr3:24536880-24536930	NHBE	bronchial:	n/a
14	chr3:24536880-24536930	HL-60	blood:	n/a
15	chr3:24536880-24536930	MCF-7	breast:	n/a
16	chr3:24536880-24536930	BE2_C	brain:	n/a
17	chr3:24536880-24536930	PFSK-1	brain:	n/a
18	chr3:24536880-24536930	AG04450	lung:	fetal
19	chr3:24536880-24536930	HCT-116	colon:	n/a
20	chr3:24536880-24536930	GM06990	blood:	n/a
21	chr3:24536880-24536930	RPTEC	kidney:	n/a
22	chr3:24536880-24536930	GM12891	blood:	n/a
23	chr3:24536880-24536930	AG09309	skin:	n/a
24	chr3:24536880-24536930	HNPCEpiC	eye:	n/a
25	chr3:24536880-24536930	ProgFib	skin:	n/a
26	chr3:24536880-24536930	HAEpiC	amniotic membrane:	n/a
27	chr3:24536880-24536930	HRE	kidney:	n/a
28	chr3:24536880-24536930	AG04449	skin:	fetal
29	chr3:24536880-24536930	HEK293	kidney:	embryo
30	chr3:24536880-24536930	PrEC	prostate:	n/a
31	chr3:24536880-24536930	GM12878	blood:	n/a
32	chr3:24536880-24536930	HRPEpiC	eye:	n/a
33	chr3:24536880-24536930	LNCaP	prostate:	n/a
34	chr3:24536880-24536930	HMEC	breast:	n/a
35	chr3:24536880-24536930	SKMC	muscle:	n/a
36	chr3:24536880-24536930	MCF10A-Er-Src	breast:	n/a
37	chr3:24536880-24536930	ECC-1	luminal epithelium:	n/a
38	chr3:24536880-24536930	HCM	heart:	n/a
39	chr3:24536880-24536930	GM19239	blood:	n/a
40	chr3:24536880-24536930	T-47D	breast:	n/a
41	chr3:24536880-24536930	SK-N-SH	brain:	n/a
42	chr3:24536880-24536930	SAEC	small airway:	n/a
43	chr3:24536880-24536930	HEEpiC	esophagus:	n/a
44	chr3:24536880-24536930	HCF	heart:	n/a
45	chr3:24536880-24536930	AoSMC	blood vessel:	n/a
46	chr3:24536880-24536930	NHDF-neo	bronchial:	n/a
47	chr3:24536880-24536930	IMR90	lung:	fetal
48	chr3:24536880-24536930	AG09319	gingival:	n/a
49	chr3:24536880-24536930	NT2-D1	testis:	n/a
50	chr3:24536880-24536930	Caco-2	colon:	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:57466622..57469005-chr3:24535228..24537121,2	MCF-7	breast:
2	chr3:15481970..15484434-chr3:24536360..24537912,2	MCF-7	breast:
3	chr3:24536865..24538833-chr6:30851271..30852816,2	MCF-7	breast:
4	chr3:23958536..23961065-chr3:24535525..24538143,3	K562	blood:
5	chr3:23846193..23848940-chr3:24535065..24537255,2	K562	blood:
6	chr3:24535191..24540424-chr3:24558354..24564929,10	K562	blood:
7	chr3:23985869..23987641-chr3:24536460..24539004,2	MCF-7	breast:
8	chr2:208031298..208032808-chr3:24536314..24538990,2	MCF-7	breast:
9	chr3:24536363..24538620-chr3:25832197..25835181,2	K562	blood:
10	chr3:23958569..23960911-chr3:24534140..24537048,3	MCF-7	breast:
11	chr3:23851889..23854305-chr3:24536164..24537886,2	K562	blood:
12	chr3:24535945..24538703-chr3:24560979..24563838,8	K562	blood:
13	chr3:24497472..24501858-chr3:24535149..24538807,5	MCF-7	breast:
14	chr3:24534533..24538643-chr3:24561395..24564731,10	MCF-7	breast:
15	chr3:24534014..24541118-chr3:24556364..24565705,22	MCF-7	breast:

Variant related genes	Relation type
THRB	TF binding region
THRB-AS1	TF binding region
THRB	CpG island
THRB-AS1	CpG island
ENSG00000118263	Chromatin interaction
ENSG00000087460	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000265028	Chromatin interaction
ENSG00000249786	Chromatin interaction
ENSG00000174748	Chromatin interaction
ENSG00000197885	Chromatin interaction
ENSG00000224822	Chromatin interaction
ENSG00000223791	Chromatin interaction
ENSG00000174738	Chromatin interaction
ENSG00000151093	Chromatin interaction
ENSG00000170142	Chromatin interaction
ENSG00000206562	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

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	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1012975	chr3:24500706-24615644	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv999384	chr3:24525345-24656873	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
5	esv3341544	chr3:24535373-24538321	Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24533600-24537200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:24533600-24537800	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr3:24533800-24537000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
4	chr3:24533800-24537400	Active TSS	Brain Angular Gyrus	brain
5	chr3:24534000-24537000	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr3:24534000-24537000	Active TSS	Stomach Smooth Muscle	stomach
7	chr3:24534200-24537000	Active TSS	Liver	Liver
8	chr3:24534400-24537000	Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr3:24534400-24538200	Active TSS	Aorta	Aorta
10	chr3:24534600-24537200	Active TSS	Psoas Muscle	Psoas
11	chr3:24534600-24537400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
12	chr3:24534600-24537600	Active TSS	Brain Anterior Caudate	brain
13	chr3:24534600-24537600	Active TSS	Brain Cingulate Gyrus	brain
14	chr3:24534800-24537200	Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr3:24534800-24537400	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr3:24534800-24537400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:24534800-24537400	Active TSS	Rectal Smooth Muscle	rectum
18	chr3:24534800-24537400	Active TSS	Stomach Mucosa	stomach
19	chr3:24535000-24537200	Active TSS	Brain Hippocampus Middle	brain
20	chr3:24535000-24537400	Active TSS	Colon Smooth Muscle	Colon
21	chr3:24535000-24537600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr3:24535000-24537600	Active TSS	Right Ventricle	heart
23	chr3:24535200-24537000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:24535200-24537000	Active TSS	Placenta Amnion	Placenta Amnion
25	chr3:24535200-24537200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:24535200-24537200	Active TSS	Rectal Mucosa Donor 31	rectum
27	chr3:24535200-24537200	Active TSS	Right Atrium	heart
28	chr3:24535200-24537200	Active TSS	HSMMtube	muscle
29	chr3:24535200-24537400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:24535200-24537400	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr3:24535200-24537400	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr3:24535200-24537400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:24535200-24537400	Active TSS	Brain Substantia Nigra	brain
34	chr3:24535200-24537400	Bivalent/Poised TSS	Fetal Thymus	thymus
35	chr3:24535200-24537400	Active TSS	NHDF-Ad	bronchial
36	chr3:24535200-24537600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:24535200-24537600	Active TSS	H9 Cell Line	embryonic stem cell
38	chr3:24535200-24537600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:24535200-24537600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:24535200-24537600	Active TSS	Fetal Lung	lung
41	chr3:24535200-24537600	Active TSS	Left Ventricle	heart
42	chr3:24535200-24537800	Active TSS	Duodenum Mucosa	Duodenum
43	chr3:24535200-24537800	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr3:24535400-24537000	Active TSS	Muscle Satellite Cultured Cells	--
45	chr3:24535400-24537000	Active TSS	Lung	lung
46	chr3:24535400-24537200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:24535400-24537200	Bivalent/Poised TSS	Colonic Mucosa	Colon
48	chr3:24535400-24537200	Active TSS	Ovary	ovary
49	chr3:24535400-24537400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
50	chr3:24535400-24537400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links