Variant report

Variant	rs3914944
Chromosome Location	chr3:24537896-24537897
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr3:24537766-24538577	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr3:24537823-24538379	K562	blood:	n/a	n/a
3	MYBL2	chr3:24537798-24538362	HepG2	liver:	n/a	n/a
4	RAD21	chr3:24537722-24538855	SK-N-SH	brain:	n/a	n/a
5	SMC3	chr3:24537794-24538434	HepG2	liver:	n/a	n/a
6	HEY1	chr3:24537879-24538357	K562	blood:	n/a	n/a
7	CTCF	chr3:24537841-24538377	HCT-116	colon:	n/a	n/a
8	BACH1	chr3:24537733-24537898	K562	blood:	n/a	n/a
9	TEAD4	chr3:24537860-24538340	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:24534554-24538147	PBDE	blood:	n/a	n/a
11	CUX1	chr3:24537657-24538307	K562	blood:	n/a	n/a
12	POLR2A	chr3:24535441-24538405	K562	blood:	n/a	n/a
13	TEAD4	chr3:24537883-24538448	K562	blood:	n/a	n/a
14	POLR2A	chr3:24537770-24538354	K562	blood:	n/a	n/a
15	ZMIZ1	chr3:24535624-24538332	K562	blood:	n/a	n/a
16	UBTF	chr3:24537854-24538429	K562	blood:	n/a	n/a
17	TCF12	chr3:24537841-24538383	A549	lung:	n/a	n/a
18	MYC	chr3:24535482-24538636	K562	blood:	n/a	chr3:24536125-24536135 chr3:24537396-24537406 chr3:24536847-24536857 chr3:24536381-24536391 chr3:24536143-24536153
19	POLR2A	chr3:24535520-24538333	K562	blood:	n/a	n/a
20	POLR2A	chr3:24537656-24537990	MCF10A-Er-Src	breast:	n/a	n/a
21	NR2F2	chr3:24537872-24538347	K562	blood:	n/a	n/a
22	MAZ	chr3:24535459-24538408	K562	blood:	n/a	chr3:24536125-24536135 chr3:24537396-24537406 chr3:24536847-24536857 chr3:24536381-24536391 chr3:24536143-24536153
23	CTCF	chr3:24537751-24538654	A549	lung:	n/a	n/a
24	HEY1	chr3:24537825-24538350	K562	blood:	n/a	n/a
25	ZBTB7A	chr3:24537872-24538360	K562	blood:	n/a	n/a
26	MYBL2	chr3:24537873-24538434	HepG2	liver:	n/a	n/a
27	GATA1	chr3:24535610-24538171	PBDE	blood:	n/a	chr3:24536736-24536744
28	RCOR1	chr3:24537819-24538467	K562	blood:	n/a	n/a
29	POLR2A	chr3:24537860-24538441	K562	blood:	n/a	n/a
30	POLR2A	chr3:24537606-24538169	HepG2	liver:	n/a	n/a
31	TBP	chr3:24535463-24538369	K562	blood:	n/a	n/a
32	POLR2A	chr3:24537850-24538433	K562	blood:	n/a	n/a
33	HDAC2	chr3:24537887-24538350	HepG2	liver:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:15481970..15484434-chr3:24536360..24537912,2	MCF-7	breast:
2	chr3:24400923..24401537-chr3:24537754..24538628,3	MCF-7	breast:
3	chr3:24305947..24306863-chr3:24537889..24538429,2	MCF-7	breast:
4	chr3:24305746..24306763-chr3:24537733..24538685,3	MCF-7	breast:
5	chr3:24536865..24538833-chr6:30851271..30852816,2	MCF-7	breast:
6	chr3:23958536..23961065-chr3:24535525..24538143,3	K562	blood:
7	chr3:24535191..24540424-chr3:24558354..24564929,10	K562	blood:
8	chr3:23985869..23987641-chr3:24536460..24539004,2	MCF-7	breast:
9	chr2:208031298..208032808-chr3:24536314..24538990,2	MCF-7	breast:
10	chr3:24536363..24538620-chr3:25832197..25835181,2	K562	blood:
11	chr3:23988541..23991177-chr3:24537846..24539360,2	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:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NR1D2-1	chr3:24537675-24538309	ENSG00000228791.3
2	lnc-THRB-3	chr3:24537763-24538504	ENSG00000272554.1

No data

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

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11918134	1.00[EUR][1000 genomes]
rs11919187	1.00[EUR][1000 genomes]
rs17014787	0.82[AFR][1000 genomes]
rs17014855	0.82[AFR][1000 genomes]
rs17014945	0.82[AFR][1000 genomes]
rs17014965	0.82[AFR][1000 genomes]
rs56083972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56339532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58351306	0.91[AFR][1000 genomes]
rs61283262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73820018	0.82[AFR][1000 genomes]
rs73820022	0.82[AFR][1000 genomes]
rs73823309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73823310	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73823329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73823330	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73823332	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73823334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73823335	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73823336	1.00[EUR][1000 genomes]
rs73823337	1.00[EUR][1000 genomes]
rs73823338	1.00[EUR][1000 genomes]
rs73823339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73823343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73823345	1.00[AFR][1000 genomes]
rs73823347	1.00[AFR][1000 genomes]
rs73823352	1.00[AFR][1000 genomes]
rs73823368	0.82[AFR][1000 genomes]
rs73823371	0.82[AFR][1000 genomes]
rs73825636	0.91[AFR][1000 genomes]
rs73825637	0.91[AFR][1000 genomes]
rs73825638	0.91[AFR][1000 genomes]
rs73825639	0.91[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	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:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24534400-24538200	Active TSS	Aorta	Aorta
2	chr3:24536600-24538800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:24537000-24538200	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr3:24537200-24538000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:24537200-24538000	Weak transcription	Fetal Heart	heart
6	chr3:24537200-24538000	Enhancers	NHLF	lung
7	chr3:24537200-24538200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:24537200-24538400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
9	chr3:24537200-24539600	Weak transcription	HSMMtube	muscle
10	chr3:24537400-24538000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:24537400-24538000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr3:24537400-24538000	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr3:24537400-24538000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr3:24537400-24538000	Bivalent Enhancer	Spleen	Spleen
15	chr3:24537400-24538000	Weak transcription	NHDF-Ad	bronchial
16	chr3:24537400-24538200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:24537400-24538200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:24537400-24538200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:24537400-24538200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
20	chr3:24537400-24538200	Flanking Active TSS	Liver	Liver
21	chr3:24537400-24538200	Enhancers	Brain Hippocampus Middle	brain
22	chr3:24537400-24538200	Bivalent Enhancer	Fetal Muscle Leg	muscle
23	chr3:24537400-24538200	Flanking Active TSS	Hela-S3	cervix
24	chr3:24537400-24538400	Enhancers	Lung	lung
25	chr3:24537400-24541800	Weak transcription	HSMM	muscle
26	chr3:24537400-24546400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:24537600-24538000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
28	chr3:24537600-24538000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:24537600-24538000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:24537600-24538000	Enhancers	Brain Anterior Caudate	brain
31	chr3:24537600-24538000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:24537600-24538000	Enhancers	Colonic Mucosa	Colon
33	chr3:24537600-24538000	Enhancers	Pancreas	Pancrea
34	chr3:24537600-24538000	Enhancers	Placenta Amnion	Placenta Amnion
35	chr3:24537600-24538000	Enhancers	Psoas Muscle	Psoas
36	chr3:24537600-24538000	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr3:24537600-24538200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
38	chr3:24537600-24538200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:24537600-24538200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:24537600-24538200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
41	chr3:24537600-24538200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:24537600-24538200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:24537600-24538200	Enhancers	Adipose Nuclei	Adipose
44	chr3:24537600-24538200	Enhancers	Placenta	Placenta
45	chr3:24537600-24538200	Enhancers	Gastric	stomach
46	chr3:24537600-24538200	Enhancers	Rectal Smooth Muscle	rectum
47	chr3:24537600-24538200	Enhancers	Right Atrium	heart
48	chr3:24537600-24538200	Enhancers	NHEK	skin
49	chr3:24537600-24538400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr3:24537600-24538400	Enhancers	HMEC	breast

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