Variant report

Variant	rs73839524
Chromosome Location	chr3:52868889-52868890
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	CEBPB	chr3:52868833-52869112	K562	blood:	n/a	n/a
2	CEBPB	chr3:52868884-52869049	HepG2	liver:	n/a	n/a
3	CEBPB	chr3:52868800-52869160	IMR90	lung:	n/a	n/a
4	POLR2A	chr3:52868839-52868954	HepG2	liver:	n/a	n/a
5	CEBPB	chr3:52868794-52869176	HepG2	liver:	n/a	n/a
6	CEBPB	chr3:52868797-52869173	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52867798..52869834-chr3:52876401..52878497,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243696	TF binding region
ITIH4	TF binding region
ENSG00000248592	Chromatin interaction
ENSG00000213533	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs17052726	1.00[AMR][1000 genomes]
rs56038605	1.00[AMR][1000 genomes]
rs60327091	1.00[AMR][1000 genomes]
rs73839120	1.00[AMR][1000 genomes]
rs73839170	1.00[AMR][1000 genomes]
rs73839528	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839530	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839531	1.00[AMR][1000 genomes]
rs73839647	1.00[AMR][1000 genomes]
rs73839653	1.00[AMR][1000 genomes]
rs73839655	1.00[AMR][1000 genomes]
rs73839660	1.00[AMR][1000 genomes]
rs73839707	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839709	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839712	1.00[AMR][1000 genomes]
rs73839714	1.00[AMR][1000 genomes]
rs73839718	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839723	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839726	1.00[AMR][1000 genomes]
rs73839727	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839774	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839776	1.00[AMR][1000 genomes]
rs73839778	1.00[AMR][1000 genomes]
rs73841131	1.00[AFR][1000 genomes];1.00[AMR][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	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52852200-52869200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr3:52852800-52869200	Weak transcription	Primary B cells from cord blood	blood
3	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:52854800-52869200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
7	chr3:52858800-52869200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:52859400-52869000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:52860200-52869000	Weak transcription	Fetal Intestine Small	intestine
10	chr3:52862000-52869200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:52863200-52872600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:52864400-52875800	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:52865000-52869400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:52865200-52869000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:52865600-52874200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:52865600-52875200	Weak transcription	Dnd41	blood
18	chr3:52865800-52869000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:52865800-52878600	Weak transcription	Small Intestine	intestine
20	chr3:52866000-52869800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:52866000-52884800	Weak transcription	HMEC	breast
22	chr3:52866200-52869000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:52866200-52869200	Weak transcription	Placenta	Placenta
24	chr3:52866200-52869600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:52866200-52870200	Weak transcription	Gastric	stomach
26	chr3:52866200-52872600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr3:52866200-52872600	Weak transcription	Esophagus	oesophagus
28	chr3:52866200-52885200	Weak transcription	NHEK	skin
29	chr3:52866400-52869800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:52866400-52871800	Strong transcription	Primary T cells from cord blood	blood
31	chr3:52866400-52872400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:52866600-52869800	Enhancers	Liver	Liver
33	chr3:52866600-52869800	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:52866600-52873600	Weak transcription	Hela-S3	cervix
35	chr3:52866600-52879200	Weak transcription	Osteobl	bone
36	chr3:52866800-52871000	Strong transcription	Spleen	Spleen
37	chr3:52866800-52872000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:52866800-52876400	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr3:52866800-52878200	Strong transcription	Fetal Brain Female	brain
40	chr3:52866800-52879600	Genic enhancers	Fetal Thymus	thymus
41	chr3:52867000-52870600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:52867000-52871000	Strong transcription	Thymus	Thymus
43	chr3:52867000-52871200	Weak transcription	Pancreas	Pancrea
44	chr3:52867000-52876400	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr3:52867000-52881600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr3:52867000-52881800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr3:52867200-52869200	Weak transcription	Aorta	Aorta
48	chr3:52867200-52871400	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr3:52867200-52875200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr3:52867400-52869000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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