Variant report

Variant	rs73840281
Chromosome Location	chr3:53270736-53270737
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	POLR2A	chr3:53269478-53270975	GM12878	blood:	n/a	n/a
2	STAT3	chr3:53270330-53270788	MCF10A-Er-Src	breast:	n/a	chr3:53270655-53270666 chr3:53270657-53270680 chr3:53270657-53270665
3	POLR2A	chr3:53270675-53270894	MCF-7	breast:	n/a	n/a
4	POLR2A	chr3:53270674-53271165	GM12891	blood:	n/a	n/a
5	POLR2A	chr3:53270091-53271086	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:53261891-53271225	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:53270613-53270927	GM12878	blood:	n/a	n/a
8	STAT3	chr3:53270249-53270824	MCF10A-Er-Src	breast:	n/a	chr3:53270655-53270666 chr3:53270657-53270680 chr3:53270657-53270665
9	POLR2A	chr3:53270588-53270924	A549	lung:	n/a	n/a
10	POLR2A	chr3:53269301-53270918	HepG2	liver:	n/a	n/a
11	MXI1	chr3:53269646-53271113	IMR90	lung:	n/a	n/a
12	POLR2A	chr3:53270008-53271065	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr3:53269992-53270911	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr3:53269866-53270905	HUVEC	blood vessel:	n/a	n/a
15	BACH1	chr3:53269846-53270741	H1-hESC	embryonic stem cell:	n/a	chr3:53270360-53270374
16	POLR2A	chr3:53269420-53271283	GM12892	blood:	n/a	n/a
17	JUND	chr3:53269511-53270803	SK-N-SH	brain:	n/a	chr3:53270363-53270370 chr3:53270363-53270371 chr3:53270361-53270373 chr3:53270363-53270371 chr3:53270362-53270372
18	POLR2A	chr3:53261940-53270977	Hela-S3	cervix:	n/a	n/a
19	MAX	chr3:53270009-53270741	SK-N-SH	brain:	n/a	chr3:53270363-53270372
20	EP300	chr3:53269950-53270807	ECC-1	luminal epithelium:	n/a	chr3:53270363-53270372 chr3:53270395-53270408
21	POLR2A	chr3:53269444-53270977	K562	blood:	n/a	n/a
22	MAZ	chr3:53269825-53270952	IMR90	lung:	n/a	chr3:53270363-53270372
23	POLR2A	chr3:53269478-53271189	A549	lung:	n/a	n/a
24	E2F6	chr3:53270056-53270781	A549	lung:	n/a	n/a
25	MAX	chr3:53270048-53270863	A549	lung:	n/a	chr3:53270363-53270372
26	BHLHE40	chr3:53270731-53270748	K562	blood:	n/a	n/a
27	EP300	chr3:53269962-53270758	A549	lung:	n/a	chr3:53270363-53270372 chr3:53270395-53270408
28	POLR2A	chr3:53269916-53270974	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:53270302-53270876	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:53269547-53270955	GM12891	blood:	n/a	n/a
31	POLR2A	chr3:53269263-53271071	HL-60	blood:	n/a	n/a
32	POLR2A	chr3:53269336-53271149	GM12891	blood:	n/a	n/a
33	POLR2A	chr3:53269901-53270981	A549	lung:	n/a	n/a
34	MAFK	chr3:53270162-53270875	Hela-S3	cervix:	n/a	chr3:53270364-53270373 chr3:53270362-53270377 chr3:53270366-53270377 chr3:53270363-53270373
35	POLR2A	chr3:53269831-53271003	GM12892	blood:	n/a	n/a
36	POLR2A	chr3:53267728-53271263	GM12892	blood:	n/a	n/a
37	MAX	chr3:53269923-53270986	A549	lung:	n/a	chr3:53270363-53270372
38	MAX	chr3:53269977-53270805	HCT-116	colon:	n/a	chr3:53270363-53270372
39	MXI1	chr3:53270160-53270879	HepG2	liver:	n/a	n/a
40	TCF12	chr3:53269836-53271271	A549	lung:	n/a	chr3:53270317-53270327 chr3:53270670-53270678
41	POLR2A	chr3:53255471-53271280	K562	blood:	n/a	n/a
42	POLR2A	chr3:53270661-53270872	A549	lung:	n/a	n/a
43	POLR2A	chr3:53270126-53270783	HCT-116	colon:	n/a	n/a
44	TCF7L2	chr3:53270190-53270945	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr3:53270583-53270928	A549	lung:	n/a	n/a
46	POLR2A	chr3:53268801-53271030	HEK293	kidney:	n/a	n/a
47	TCF12	chr3:53269972-53270791	ECC-1	luminal epithelium:	n/a	chr3:53270317-53270327 chr3:53270670-53270678
48	RCOR1	chr3:53269235-53271008	IMR90	lung:	n/a	n/a
49	POLR2A	chr3:53269960-53270798	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr3:53270005-53270786	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:53268810..53273941-chr3:53286770..53291307,7	MCF-7	breast:
2	chr3:53268759..53271558-chr3:53275387..53277889,3	MCF-7	breast:
3	chr3:53268931..53277907-chr3:53285563..53291617,11	MCF-7	breast:
4	chr3:53266350..53272175-chr3:53273806..53279972,8	K562	blood:
5	chr3:53148133..53149133-chr3:53270420..53271199,2	K562	blood:

Variant related genes	Relation type
TKT	TF binding region
ENSG00000163931	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs55739626	1.00[AMR][1000 genomes]
rs55797425	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56138740	1.00[AMR][1000 genomes]
rs57085673	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57188310	1.00[AMR][1000 genomes]
rs57320366	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57530569	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58006923	1.00[AMR][1000 genomes]
rs58191586	1.00[AMR][1000 genomes]
rs58563464	1.00[AMR][1000 genomes]
rs60407612	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60891705	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72957562	1.00[AMR][1000 genomes]
rs73840218	1.00[AMR][1000 genomes]
rs73840219	1.00[AMR][1000 genomes]
rs73840220	1.00[AMR][1000 genomes]
rs73840224	1.00[AMR][1000 genomes]
rs73840228	1.00[AMR][1000 genomes]
rs73840236	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73840239	1.00[AMR][1000 genomes]
rs73840247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73840260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73840298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843106	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843108	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843110	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843111	1.00[AMR][1000 genomes]
rs73843112	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843113	1.00[AMR][1000 genomes]
rs73843115	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843117	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843118	0.93[AFR][1000 genomes]
rs73843120	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843121	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843124	1.00[AMR][1000 genomes]
rs73843127	1.00[AMR][1000 genomes]
rs73843129	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843130	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843148	1.00[AMR][1000 genomes]
rs874586	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53255600-53274400	Strong transcription	GM12878-XiMat	blood
2	chr3:53256400-53272400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:53256400-53276400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:53256400-53276600	Strong transcription	Fetal Brain Female	brain
5	chr3:53256400-53276800	Strong transcription	Fetal Stomach	stomach
6	chr3:53256600-53272000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:53256800-53272200	Strong transcription	Brain Germinal Matrix	brain
8	chr3:53256800-53276600	Strong transcription	Thymus	Thymus
9	chr3:53256800-53277000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:53256800-53277000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:53257000-53276800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:53257000-53276800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:53257000-53277800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:53257200-53271000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:53257200-53276200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:53257200-53276600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:53257400-53276200	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:53257400-53276600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr3:53257400-53277200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:53257400-53278800	Strong transcription	Primary T cells from cord blood	blood
21	chr3:53257400-53280200	Strong transcription	Dnd41	blood
22	chr3:53257600-53276400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:53257600-53276800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:53257800-53276600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:53258200-53276800	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr3:53258400-53276800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:53258600-53271000	Strong transcription	Fetal Lung	lung
28	chr3:53258600-53276600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:53260200-53272400	Weak transcription	Fetal Brain Male	brain
30	chr3:53263000-53272200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr3:53263000-53274000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:53263200-53274400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:53265600-53271200	Genic enhancers	Spleen	Spleen
34	chr3:53265800-53271200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:53266200-53273600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr3:53266400-53272600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:53266800-53271200	Genic enhancers	HSMM	muscle
38	chr3:53266800-53276600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:53266800-53279000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:53267200-53271600	Genic enhancers	Primary monocytes fromperipheralblood	blood
41	chr3:53267200-53272800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
42	chr3:53268200-53276600	Strong transcription	Primary B cells from cord blood	blood
43	chr3:53269000-53271000	Genic enhancers	Right Ventricle	heart
44	chr3:53269200-53272400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr3:53269400-53272800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:53269400-53273000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr3:53269400-53275200	Genic enhancers	HUVEC	blood vessel
48	chr3:53269400-53276600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:53269600-53270800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:53269600-53271000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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