Variant report

Variant	rs12297433
Chromosome Location	chr12:49621412-49621413
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	REST	chr12:49621219-49622384	H1-neurons	neurons:	n/a	chr12:49621881-49621891

No.	Distal block	Cell Line	Cell type
1	chr12:49519485..49526890-chr12:49616239..49624332,15	K562	blood:
2	chr12:49523171..49526001-chr12:49621210..49624929,3	MCF-7	breast:
3	chr12:49581406..49583552-chr12:49621389..49622908,2	MCF-7	breast:
4	chr12:49619902..49623805-chr12:49655877..49662372,6	K562	blood:
5	chr12:49513866..49528454-chr12:49616957..49635747,92	K562	blood:

Variant related genes	Relation type
TUBA1C	TF binding region
ENSG00000167553	Chromatin interaction
ENSG00000167552	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000258101	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10047512	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10047588	1.00[AMR][1000 genomes]
rs1109811	1.00[AMR][1000 genomes]
rs11168925	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168927	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168928	1.00[AMR][1000 genomes]
rs11168931	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs11168938	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs11168939	1.00[AMR][1000 genomes]
rs11168940	1.00[AMR][1000 genomes]
rs11168942	1.00[AMR][1000 genomes]
rs11168955	1.00[YRI][hapmap]
rs12296231	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs12296536	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12300386	1.00[AMR][1000 genomes]
rs12300998	1.00[AMR][1000 genomes]
rs12303188	0.88[YRI][hapmap]
rs12304259	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs12304483	1.00[AMR][1000 genomes]
rs12304746	1.00[AMR][1000 genomes]
rs12309028	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12314967	1.00[AMR][1000 genomes]
rs12318666	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12322876	1.00[AMR][1000 genomes]
rs28758893	1.00[AMR][1000 genomes]
rs9804936	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	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	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv518041	chr12:49618043-49645240	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49610200-49625800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:49615200-49625600	Weak transcription	Placenta	Placenta
3	chr12:49616800-49624400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr12:49616800-49625800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:49616800-49626000	Weak transcription	Adipose Nuclei	Adipose
6	chr12:49617000-49624000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr12:49617600-49625600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:49617600-49625800	Weak transcription	NHDF-Ad	bronchial
9	chr12:49617600-49626000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:49619200-49624000	Weak transcription	Primary B cells from cord blood	blood
11	chr12:49619800-49624600	Weak transcription	HSMM	muscle
12	chr12:49619800-49627200	Weak transcription	Lung	lung
13	chr12:49620000-49622400	Weak transcription	K562	blood
14	chr12:49620000-49623400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:49620000-49624000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr12:49620000-49626000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:49620200-49623200	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr12:49620200-49623400	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr12:49620600-49622000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr12:49620600-49622000	Enhancers	HSMMtube	muscle
21	chr12:49620800-49621600	Enhancers	Fetal Brain Male	brain
22	chr12:49620800-49622200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:49621000-49621600	Enhancers	Brain Germinal Matrix	brain
24	chr12:49621000-49621800	Enhancers	Fetal Muscle Leg	muscle
25	chr12:49621000-49622000	Enhancers	Brain Hippocampus Middle	brain
26	chr12:49621200-49622000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:49621200-49625400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr12:49621400-49621600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:49621400-49622000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr12:49621400-49622000	Enhancers	Brain Anterior Caudate	brain
31	chr12:49621400-49622000	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr12:49621400-49622000	Enhancers	Brain Substantia Nigra	brain
33	chr12:49621400-49622200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:49621400-49622200	Enhancers	Brain Cingulate Gyrus	brain
35	chr12:49621400-49622600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:49621400-49622600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:49621400-49622800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:49621400-49622800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:49621400-49622800	Enhancers	Brain Angular Gyrus	brain
40	chr12:49621400-49623400	Active TSS	Fetal Brain Female	brain

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