Variant report

Variant	rs35778241
Chromosome Location	chr3:24537478-24537479
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	CTCF	chr3:24535467-24537699	A549	lung:	n/a	chr3:24536750-24536759 chr3:24535554-24535567 chr3:24536379-24536392 chr3:24536385-24536398
2	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
3	HEY1	chr3:24535449-24537529	K562	blood:	n/a	chr3:24536750-24536765 chr3:24536479-24536494 chr3:24536491-24536506 chr3:24536707-24536722 chr3:24536792-24536807
4	YY1	chr3:24537149-24537558	A549	lung:	n/a	chr3:24537392-24537403 chr3:24537405-24537415 chr3:24537395-24537404
5	MAX	chr3:24536916-24537537	MCF-7	breast:	n/a	chr3:24537396-24537406
6	ZEB1	chr3:24535519-24537509	HepG2	liver:	n/a	chr3:24536969-24536980
7	CREB1	chr3:24535582-24537508	K562	blood:	n/a	n/a
8	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
9	MAX	chr3:24535349-24537594	K562	blood:	n/a	chr3:24536125-24536135 chr3:24537396-24537406 chr3:24536847-24536857 chr3:24536381-24536391 chr3:24536143-24536153
10	PML	chr3:24536548-24537517	K562	blood:	n/a	n/a
11	POLR2A	chr3:24535466-24537678	K562	blood:	n/a	n/a
12	NR2F2	chr3:24536111-24537511	K562	blood:	n/a	n/a
13	TAF1	chr3:24536073-24537496	K562	blood:	n/a	n/a
14	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
15	MAZ	chr3:24535500-24537843	HepG2	liver:	n/a	chr3:24536125-24536135 chr3:24537396-24537406 chr3:24536847-24536857 chr3:24536381-24536391 chr3:24536143-24536153
16	POLR2A	chr3:24535758-24537506	K562	blood:	n/a	n/a
17	MAX	chr3:24535656-24537640	HCT-116	colon:	n/a	chr3:24536125-24536135 chr3:24537396-24537406 chr3:24536847-24536857 chr3:24536381-24536391 chr3:24536143-24536153
18	ELF1	chr3:24537278-24537692	K562	blood:	n/a	chr3:24537512-24537525
19	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
20	POLR2A	chr3:24535405-24537667	HepG2	liver:	n/a	n/a
21	TEAD4	chr3:24536807-24537544	K562	blood:	n/a	n/a
22	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
23	SMARCC1	chr3:24535422-24537518	Hela-S3	cervix:	n/a	n/a
24	TAF1	chr3:24536788-24537629	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr3:24535504-24537653	K562	blood:	n/a	n/a
26	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
27	POLR2A	chr3:24535410-24537534	K562	blood:	n/a	n/a
28	MYC	chr3:24535387-24537606	K562	blood:	n/a	chr3:24536125-24536135 chr3:24537396-24537406 chr3:24536847-24536857 chr3:24536381-24536391 chr3:24536143-24536153
29	NR2F2	chr3:24536444-24537485	MCF-7	breast:	n/a	n/a
30	POLR2A	chr3:24536227-24537521	HCT-116	colon:	n/a	n/a
31	YY1	chr3:24535625-24537504	K562	blood:	n/a	chr3:24536946-24536960 chr3:24536717-24536726 chr3:24537392-24537403 chr3:24536791-24536805 chr3:24536793-24536804 chr3:24536394-24536403 chr3:24537405-24537415 chr3:24536790-24536799 chr3:24537395-24537404 chr3:24536796-24536805 chr3:24536790-24536801 chr3:24536720-24536729 chr3:24536793-24536802 chr3:24536406-24536420 chr3:24536794-24536808
32	MYBL2	chr3:24536873-24537595	HepG2	liver:	n/a	n/a
33	ZNF263	chr3:24535354-24537587	HEK293-T-REx	kidney:	n/a	chr3:24537226-24537235 chr3:24536385-24536394 chr3:24536129-24536138 chr3:24537115-24537136
34	TEAD4	chr3:24535742-24537511	ECC-1	luminal epithelium:	n/a	n/a
35	MAX	chr3:24535597-24537533	MCF-7	breast:	n/a	chr3:24536125-24536135 chr3:24537396-24537406 chr3:24536847-24536857 chr3:24536381-24536391 chr3:24536143-24536153
36	TCF12	chr3:24536833-24537498	ECC-1	luminal epithelium:	n/a	chr3:24536971-24536978 chr3:24536957-24536964 chr3:24537083-24537090
37	RCOR1	chr3:24535262-24537500	K562	blood:	n/a	n/a
38	YY1	chr3:24535673-24537515	HepG2	liver:	n/a	chr3:24536946-24536960 chr3:24536717-24536726 chr3:24537392-24537403 chr3:24536791-24536805 chr3:24536793-24536804 chr3:24536394-24536403 chr3:24537405-24537415 chr3:24536790-24536799 chr3:24537395-24537404 chr3:24536796-24536805 chr3:24536790-24536801 chr3:24536720-24536729 chr3:24536793-24536802 chr3:24536406-24536420 chr3:24536794-24536808
39	POLR2A	chr3:24535677-24537572	K562	blood:	n/a	n/a
40	POLR2A	chr3:24535682-24537621	K562	blood:	n/a	n/a
41	POLR2A	chr3:24535459-24537514	HepG2	liver:	n/a	n/a
42	TAF7	chr3:24536730-24537554	K562	blood:	n/a	n/a
43	ARID3A	chr3:24537363-24537748	K562	blood:	n/a	n/a
44	MAX	chr3:24535335-24537639	HepG2	liver:	n/a	chr3:24536125-24536135 chr3:24537396-24537406 chr3:24536847-24536857 chr3:24536381-24536391 chr3:24536143-24536153
45	POLR2A	chr3:24535470-24537527	MCF-7	breast:	n/a	n/a
46	TAF1	chr3:24535751-24537504	HepG2	liver:	n/a	n/a
47	POLR2A	chr3:24535390-24537647	MCF-7	breast:	n/a	n/a
48	TBL1XR1	chr3:24536766-24537550	K562	blood:	n/a	n/a
49	EGR1	chr3:24535549-24537704	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
50	POLR2A	chr3:24534554-24538147	PBDE	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:24537469-24537519	Jurkat	blood:	n/a
2	chr3:24537469-24537519	HCPEpiC	choroid plexus:	n/a
3	chr3:24537469-24537519	HRE	kidney:	n/a
4	chr3:24537469-24537519	HPAEpiC	pulmonary alveolar:	n/a
5	chr3:24537469-24537519	BJ	skin:	n/a
6	chr3:24537469-24537519	NB4	blood:	n/a
7	chr3:24537469-24537519	A549	lung:	n/a
8	chr3:24537469-24537519	HUVEC	blood vessel:	n/a
9	chr3:24537469-24537519	NH-A	brain:	n/a
10	chr3:24537469-24537519	NHDF-neo	bronchial:	n/a
11	chr3:24537469-24537519	U87	brain:	n/a
12	chr3:24537469-24537519	T-47D	breast:	n/a
13	chr3:24537469-24537519	HEK293	kidney:	embryo
14	chr3:24537469-24537519	HAEpiC	amniotic membrane:	n/a
15	chr3:24537469-24537519	HMEC	breast:	n/a
16	chr3:24537469-24537519	HRPEpiC	eye:	n/a
17	chr3:24537469-24537519	NHBE	bronchial:	n/a
18	chr3:24537469-24537519	HCM	heart:	n/a
19	chr3:24537469-24537519	AG04450	lung:	fetal
20	chr3:24537469-24537519	ProgFib	skin:	n/a
21	chr3:24537469-24537519	HCT-116	colon:	n/a
22	chr3:24537469-24537519	HIPEpiC	eye:	n/a
23	chr3:24537469-24537519	AG09309	skin:	n/a
24	chr3:24537469-24537519	SK-N-SH_RA	brain:	n/a
25	chr3:24537469-24537519	Hepatocyte	liver:	n/a
26	chr3:24537469-24537519	CMK	blood:	n/a
27	chr3:24537469-24537519	HCF	heart:	n/a
28	chr3:24537469-24537519	H1-hESC	embryonic stem cell:	embryo
29	chr3:24537469-24537519	LNCaP	prostate:	n/a
30	chr3:24537469-24537519	SKMC	muscle:	n/a
31	chr3:24537469-24537519	SK-N-MC	brain:	n/a
32	chr3:24537469-24537519	GM12878	blood:	n/a
33	chr3:24537469-24537519	PANC-1	pancreas:	n/a
34	chr3:24537469-24537519	ovcar-3	ovarian:	n/a
35	chr3:24537469-24537519	K562	blood:	n/a
36	chr3:24537469-24537519	PFSK-1	brain:	n/a
37	chr3:24537469-24537519	AG04449	skin:	fetal
38	chr3:24537469-24537519	AG10803	skin:	n/a
39	chr3:24537469-24537519	NT2-D1	testis:	n/a
40	chr3:24537469-24537519	AoSMC	blood vessel:	n/a
41	chr3:24537469-24537519	PrEC	prostate:	n/a
42	chr3:24537469-24537519	HepG2	liver:	n/a
43	chr3:24537469-24537519	HRCEpiC	kidney:	n/a
44	chr3:24537469-24537519	SK-N-SH	brain:	n/a
45	chr3:24537469-24537519	HEEpiC	esophagus:	n/a
46	chr3:24537469-24537519	MCF10A-Er-Src	breast:	n/a
47	chr3:24537469-24537519	RPTEC	kidney:	n/a
48	chr3:24537469-24537519	IMR90	lung:	fetal
49	chr3:24537469-24537519	GM19239	blood:	n/a
50	chr3:24537469-24537519	AG09319	gingival:	n/a

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NR1D2-1	chr3:24537448-24537675	ENSG00000228791.3

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

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs13090120	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749376	0.82[EUR][1000 genomes]
rs4858621	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58016799	1.00[ASN][1000 genomes]
rs6803476	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805614	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71328481	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][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	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:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24533600-24537800	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr3:24534400-24538200	Active TSS	Aorta	Aorta
3	chr3:24534600-24537600	Active TSS	Brain Anterior Caudate	brain
4	chr3:24534600-24537600	Active TSS	Brain Cingulate Gyrus	brain
5	chr3:24535000-24537600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr3:24535000-24537600	Active TSS	Right Ventricle	heart
7	chr3:24535200-24537600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:24535200-24537600	Active TSS	H9 Cell Line	embryonic stem cell
9	chr3:24535200-24537600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:24535200-24537600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:24535200-24537600	Active TSS	Fetal Lung	lung
12	chr3:24535200-24537600	Active TSS	Left Ventricle	heart
13	chr3:24535200-24537800	Active TSS	Duodenum Mucosa	Duodenum
14	chr3:24535200-24537800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr3:24535400-24537600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr3:24535400-24537600	Active TSS	Esophagus	oesophagus
17	chr3:24535400-24537600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
18	chr3:24535600-24537600	Active TSS	Pancreas	Pancrea
19	chr3:24535600-24537800	Active TSS	K562	blood
20	chr3:24535800-24537600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:24535800-24537600	Active TSS	A549	lung
22	chr3:24536000-24537600	Bivalent Enhancer	Fetal Brain Male	brain
23	chr3:24536200-24537800	Active TSS	Fetal Intestine Small	intestine
24	chr3:24536400-24537800	Active TSS	HepG2	liver
25	chr3:24536600-24537800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:24536600-24538800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:24536800-24537600	Flanking Active TSS	HMEC	breast
28	chr3:24537000-24537600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
29	chr3:24537000-24537600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:24537000-24537600	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr3:24537000-24537600	Flanking Active TSS	Placenta	Placenta
32	chr3:24537000-24537600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
33	chr3:24537000-24537600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr3:24537000-24537800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:24537000-24537800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr3:24537000-24538200	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr3:24537200-24537600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:24537200-24537600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:24537200-24537800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr3:24537200-24538000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:24537200-24538000	Weak transcription	Fetal Heart	heart
42	chr3:24537200-24538000	Enhancers	NHLF	lung
43	chr3:24537200-24538200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:24537200-24538400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr3:24537200-24539600	Weak transcription	HSMMtube	muscle
46	chr3:24537400-24537600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
47	chr3:24537400-24537600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:24537400-24537600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
49	chr3:24537400-24537600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
50	chr3:24537400-24537600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links