Variant report

Variant	rs12299500
Chromosome Location	chr12:49527650-49527651
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49527496-49527727	HepG2	liver:	n/a	n/a
2	CEBPB	chr12:49527612-49527788	HepG2	liver:	n/a	chr12:49527666-49527677
3	CEBPB	chr12:49527491-49527804	Hela-S3	cervix:	n/a	chr12:49527666-49527677
4	EGR1	chr12:49527558-49527765	K562	blood:	n/a	n/a
5	EGR1	chr12:49527553-49527804	K562	blood:	n/a	n/a
6	CEBPB	chr12:49527637-49527807	K562	blood:	n/a	chr12:49527666-49527677

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49477289..49493962-chr12:49512467..49528127,64	K562	blood:
2	chr12:49411218..49412872-chr12:49527413..49529313,2	K562	blood:
3	chr12:49523107..49527860-chr12:49656151..49664210,14	MCF-7	breast:
4	chr12:49513866..49528454-chr12:49616957..49635747,92	K562	blood:
5	chr12:49440399..49469923-chr12:49518291..49528303,83	K562	blood:
6	chr12:49519914..49528393-chr12:49656527..49662615,75	K562	blood:
7	chr12:49450455..49459531-chr12:49522374..49527837,16	MCF-7	breast:
8	chr12:49493937..49507579-chr12:49519161..49528577,46	K562	blood:
9	chr12:49451508..49465481-chr12:49521303..49528986,40	MCF-7	breast:
10	chr12:49446392..49469923-chr12:49518127..49527853,66	K562	blood:

No data

Variant related genes	Relation type
ENSG00000200309	TF binding region
TUBA1B	TF binding region
ENSG00000139549	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000167550	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10083069	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10160974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11168879	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12303622	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12308393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12315499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12317546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12318545	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12321116	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3842281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61730859	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	esv3417605	chr12:49521878-49578961	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49525600-49528000	Flanking Active TSS	Hela-S3	cervix
2	chr12:49526000-49527800	Enhancers	Primary B cells from peripheral blood	blood
3	chr12:49526000-49527800	Enhancers	Fetal Intestine Small	intestine
4	chr12:49526200-49531200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:49526400-49527800	Enhancers	Fetal Brain Male	brain
6	chr12:49526400-49527800	Enhancers	Fetal Muscle Leg	muscle
7	chr12:49526400-49527800	Enhancers	Fetal Thymus	thymus
8	chr12:49526400-49528600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr12:49526800-49527800	Enhancers	Placenta	Placenta
10	chr12:49526800-49528000	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr12:49527000-49527800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:49527000-49527800	Enhancers	Small Intestine	intestine
13	chr12:49527000-49528000	Enhancers	HepG2	liver
14	chr12:49527000-49530600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr12:49527000-49532000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:49527000-49532400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr12:49527000-49533000	Weak transcription	Fetal Stomach	stomach
18	chr12:49527000-49534400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:49527000-49555200	Weak transcription	Thymus	Thymus
20	chr12:49527200-49527800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr12:49527200-49527800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:49527200-49527800	Enhancers	Ovary	ovary
23	chr12:49527200-49528000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:49527200-49531400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:49527200-49531800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:49527200-49533000	Weak transcription	Fetal Brain Female	brain
27	chr12:49527400-49527800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:49527400-49527800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:49527400-49527800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:49527400-49527800	Enhancers	HMEC	breast
31	chr12:49527600-49527800	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr12:49527600-49527800	Enhancers	Muscle Satellite Cultured Cells	--
33	chr12:49527600-49527800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:49527600-49527800	Enhancers	Adipose Nuclei	Adipose
35	chr12:49527600-49527800	Enhancers	Brain Angular Gyrus	brain
36	chr12:49527600-49527800	Enhancers	Duodenum Mucosa	Duodenum
37	chr12:49527600-49527800	Enhancers	Right Ventricle	heart
38	chr12:49527600-49527800	Flanking Active TSS	Dnd41	blood
39	chr12:49527600-49528000	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr12:49527600-49528000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:49527600-49528000	Enhancers	GM12878-XiMat	blood
42	chr12:49527600-49531200	Weak transcription	Fetal Lung	lung
43	chr12:49527600-49531400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:49527600-49532000	Weak transcription	K562	blood
45	chr12:49527600-49532200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr12:49527600-49532600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:49527600-49542400	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links