Variant report

Variant	rs13092720
Chromosome Location	chr3:48700730-48700731
allele	A/G
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	MYC	chr3:48700707-48701665	MCF-7	breast:	n/a	chr3:48701108-48701118
2	MAX	chr3:48700139-48701833	MCF-7	breast:	n/a	chr3:48701108-48701118 chr3:48700391-48700400
3	HEY1	chr3:48700248-48701264	HepG2	liver:	n/a	n/a
4	MYC	chr3:48700314-48701781	K562	blood:	n/a	chr3:48701108-48701118 chr3:48700391-48700400
5	CHD1	chr3:48700186-48701447	H1-hESC	embryonic stem cell:	n/a	chr3:48700301-48700311 chr3:48700865-48700875
6	YY1	chr3:48700157-48701797	SK-N-SH	brain:	n/a	chr3:48700424-48700432 chr3:48700423-48700445 chr3:48700421-48700440 chr3:48700309-48700329 chr3:48700305-48700327 chr3:48700423-48700433 chr3:48700316-48700324 chr3:48700426-48700434 chr3:48701013-48701027
7	POLR2A	chr3:48700252-48701781	HEK293	kidney:	n/a	n/a
8	POLR2A	chr3:48700505-48701866	K562	blood:	n/a	n/a
9	TCF12	chr3:48700233-48702045	A549	lung:	n/a	n/a
10	POLR2A	chr3:48700118-48701900	SK-N-SH	brain:	n/a	n/a
11	TEAD4	chr3:48700121-48701936	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr3:48699598-48702057	U87	brain:	n/a	n/a
13	POLR2A	chr3:48700158-48701979	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr3:48700210-48701755	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr3:48700337-48701828	K562	blood:	n/a	n/a
16	SP1	chr3:48700671-48701939	A549	lung:	n/a	chr3:48701038-48701047 chr3:48701279-48701293 chr3:48701037-48701046 chr3:48701633-48701642 chr3:48701308-48701320 chr3:48701036-48701047 chr3:48701278-48701290 chr3:48701279-48701288 chr3:48701632-48701641 chr3:48701279-48701289 chr3:48701279-48701288 chr3:48701631-48701643 chr3:48701278-48701290 chr3:48701036-48701048 chr3:48701308-48701320 chr3:48701279-48701289 chr3:48701631-48701643 chr3:48701305-48701319 chr3:48701280-48701289 chr3:48701037-48701046 chr3:48701309-48701318 chr3:48701582-48701603 chr3:48701628-48701642
17	YY1	chr3:48700182-48700832	GM12878	blood:	n/a	chr3:48700424-48700432 chr3:48700423-48700445 chr3:48700421-48700440 chr3:48700309-48700329 chr3:48700305-48700327 chr3:48700423-48700433 chr3:48700316-48700324 chr3:48700426-48700434
18	MYC	chr3:48700169-48701828	A549	lung:	n/a	chr3:48701108-48701118 chr3:48700391-48700400
19	POLR2A	chr3:48698903-48702611	H1-hESC	embryonic stem cell:	n/a	n/a
20	SIX5	chr3:48700159-48701152	A549	lung:	n/a	n/a
21	CHD2	chr3:48700430-48701698	K562	blood:	n/a	chr3:48700865-48700875
22	POLR2A	chr3:48700321-48701625	K562	blood:	n/a	n/a
23	POLR2A	chr3:48700175-48701825	H1-hESC	embryonic stem cell:	n/a	n/a
24	SIN3AK20	chr3:48700720-48701863	H1-hESC	embryonic stem cell:	n/a	n/a
25	E2F6	chr3:48700189-48701898	H1-hESC	embryonic stem cell:	n/a	chr3:48701583-48701592 chr3:48701632-48701641 chr3:48701571-48701580 chr3:48701847-48701856 chr3:48700263-48700275
26	POLR2A	chr3:48700176-48701948	GM12878	blood:	n/a	n/a
27	POLR2A	chr3:48700196-48701901	PFSK-1	brain:	n/a	n/a
28	MAX	chr3:48700591-48701381	K562	blood:	n/a	chr3:48701108-48701118
29	FOSL2	chr3:48700423-48701828	A549	lung:	n/a	chr3:48701570-48701579 chr3:48701631-48701640
30	MAX	chr3:48700206-48701841	K562	blood:	n/a	chr3:48701108-48701118 chr3:48700391-48700400
31	POLR2A	chr3:48700169-48701742	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr3:48700197-48701831	Hela-S3	cervix:	n/a	n/a
33	USF2	chr3:48700545-48701837	Hela-S3	cervix:	n/a	n/a
34	TCF12	chr3:48700669-48701827	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr3:48700239-48701870	HepG2	liver:	n/a	n/a
36	REST	chr3:48700104-48701807	U87	brain:	n/a	chr3:48700747-48700767 chr3:48700550-48700563 chr3:48700448-48700466 chr3:48700747-48700761 chr3:48700547-48700560 chr3:48700447-48700467 chr3:48700453-48700467 chr3:48700547-48700556
37	REST	chr3:48700104-48701809	U87	brain:	n/a	chr3:48700747-48700767 chr3:48700550-48700563 chr3:48700448-48700466 chr3:48700747-48700761 chr3:48700547-48700560 chr3:48700447-48700467 chr3:48700453-48700467 chr3:48700547-48700556
38	MYC	chr3:48700240-48701794	K562	blood:	n/a	chr3:48701108-48701118 chr3:48700391-48700400
39	MAZ	chr3:48700151-48701896	IMR90	lung:	n/a	chr3:48701108-48701118 chr3:48700391-48700400
40	TBL1XR1	chr3:48700583-48701566	K562	blood:	n/a	n/a
41	TAF7	chr3:48700204-48701860	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr3:48700255-48701891	IMR90	lung:	n/a	n/a
43	JUND	chr3:48700668-48701801	Hela-S3	cervix:	n/a	chr3:48701570-48701579 chr3:48701631-48701640
44	POLR2A	chr3:48700254-48701606	A549	lung:	n/a	n/a
45	POLR2A	chr3:48700200-48702086	SK-N-MC	brain:	n/a	n/a
46	PBX3	chr3:48700156-48701922	SK-N-SH	brain:	n/a	chr3:48701848-48701857 chr3:48701584-48701593 chr3:48701170-48701179
47	HCFC1	chr3:48700208-48701818	K562	blood:	n/a	n/a
48	RFX5	chr3:48700039-48702079	SK-N-SH	brain:	n/a	chr3:48701848-48701857 chr3:48701584-48701593
49	POLR2A	chr3:48700115-48701814	MCF-7	breast:	n/a	n/a
50	POLR2A	chr3:48700001-48701854	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48670997..48674874-chr3:48698947..48702118,7	MCF-7	breast:
2	chr3:48699299..48703873-chr3:48715927..48726939,20	MCF-7	breast:
3	chr3:48700692..48701281-chr8:146017898..146018600,2	HCT-116	colon:
4	chr3:48678137..48679650-chr3:48699747..48701923,2	MCF-7	breast:
5	chr3:48698129..48704726-chr3:48706101..48715056,13	MCF-7	breast:
6	chr3:48488018..48489854-chr3:48700311..48702050,2	K562	blood:
7	chr3:48700180..48704062-chr3:48721751..48723924,3	K562	blood:
8	chr3:48700292..48701937-chr3:48721950..48724599,2	K562	blood:
9	chr12:53472772..53473360-chr3:48700433..48700978,2	Hela-S3	cervix:
10	chr3:48680179..48682493-chr3:48699784..48702712,4	MCF-7	breast:
11	chr3:48699555..48701541-chr3:49130676..49133286,2	K562	blood:
12	chr3:48698351..48700757-chr3:49057854..49060697,2	K562	blood:
13	chr3:48699257..48701574-chr3:49057854..49059590,2	K562	blood:
14	chr3:48699840..48702093-chr3:49056482..49059004,2	MCF-7	breast:
15	chr3:48699225..48701604-chr3:48731929..48734312,2	MCF-7	breast:
16	chr3:48670764..48674544-chr3:48699167..48702803,6	K562	blood:
17	chr3:48670764..48674544-chr3:48698929..48702803,9	K562	blood:
18	chr15:35261395..35262156-chr3:48700550..48701362,2	Hela-S3	cervix:
19	chr3:48647141..48648853-chr3:48697785..48700969,3	MCF-7	breast:
20	chr3:48540047..48541842-chr3:48700022..48702495,2	MCF-7	breast:
21	chr3:48700630..48703207-chr3:49044613..49046334,2	K562	blood:
22	chr3:48698738..48703197-chr3:48713751..48717809,8	K562	blood:
23	chr3:48667529..48675453-chr3:48697968..48703139,10	MCF-7	breast:
24	chr16:11836302..11836972-chr3:48700374..48700912,2	HCT-116	colon:
25	chr3:48700103..48702620-chr3:48955233..48957367,3	K562	blood:
26	chr3:48699573..48703813-chr3:48719476..48724654,10	MCF-7	breast:
27	chr3:48593030..48597118-chr3:48698507..48702121,6	MCF-7	breast:
28	chr3:48663872..48666244-chr3:48699915..48701423,2	K562	blood:
29	chr3:48669152..48670983-chr3:48700604..48702658,2	MCF-7	breast:
30	chr3:48678987..48680520-chr3:48698680..48701564,2	K562	blood:

Variant related genes	Relation type
CELSR3	TF binding region
ENSG00000228350	TF binding region
ENSG00000225697	Chromatin interaction
ENSG00000178252	Chromatin interaction
ENSG00000164054	Chromatin interaction
ENSG00000153066	Chromatin interaction
ENSG00000167778	Chromatin interaction
ENSG00000263898	Chromatin interaction
ENSG00000010256	Chromatin interaction
ENSG00000161016	Chromatin interaction
ENSG00000271973	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000021776	Chromatin interaction
ENSG00000221883	Chromatin interaction
ENSG00000114268	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000177479	Chromatin interaction
ENSG00000164053	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000244380	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000068745	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs34416066	0.87[ASN][1000 genomes]
rs34798641	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv876763	chr3:48669648-48710310	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	esv3409347	chr3:48697698-48701896	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48698400-48700800	Enhancers	Lung	lung
2	chr3:48698400-48701800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr3:48698600-48701800	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr3:48698600-48702400	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr3:48698800-48701600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr3:48698800-48701800	Active TSS	H1 Cell Line	embryonic stem cell
7	chr3:48698800-48701800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:48698800-48701800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:48698800-48701800	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr3:48698800-48702000	Active TSS	H9 Cell Line	embryonic stem cell
11	chr3:48699000-48701600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:48699000-48701800	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr3:48699000-48701800	Active TSS	Brain Hippocampus Middle	brain
14	chr3:48699000-48701800	Active TSS	Brain Substantia Nigra	brain
15	chr3:48699000-48702000	Active TSS	Brain Angular Gyrus	brain
16	chr3:48699000-48702000	Active TSS	Brain Anterior Caudate	brain
17	chr3:48699000-48702000	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr3:48699000-48702200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:48699200-48700800	Bivalent Enhancer	Fetal Thymus	thymus
20	chr3:48699200-48701600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:48699200-48701800	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr3:48699200-48701800	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr3:48699400-48701000	Enhancers	Pancreas	Pancrea
24	chr3:48699600-48700800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:48699600-48701600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:48699600-48702000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:48699800-48701000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:48699800-48701600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:48699800-48701600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:48699800-48701600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:48699800-48701800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:48699800-48701800	Active TSS	Fetal Brain Female	brain
33	chr3:48699800-48701800	Active TSS	A549	lung
34	chr3:48700000-48700800	Bivalent/Poised TSS	Fetal Stomach	stomach
35	chr3:48700000-48701600	Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr3:48700000-48701800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:48700000-48701800	Active TSS	Brain Germinal Matrix	brain
38	chr3:48700200-48700800	Active TSS	Ovary	ovary
39	chr3:48700200-48700800	ZNF genes & repeats	Spleen	Spleen
40	chr3:48700200-48701000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
41	chr3:48700200-48701000	Bivalent Enhancer	Left Ventricle	heart
42	chr3:48700200-48701200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
43	chr3:48700200-48701200	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:48700200-48701200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:48700200-48701400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
46	chr3:48700200-48701600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:48700200-48701600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
48	chr3:48700200-48701600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
49	chr3:48700200-48701600	Flanking Active TSS	Placenta	Placenta
50	chr3:48700200-48701600	Flanking Active TSS	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links