Variant report

Variant	rs9804936
Chromosome Location	chr12:49621266-49621267
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	chr12:49619902..49623805-chr12:49655877..49662372,6	K562	blood:
4	chr12:49513866..49528454-chr12:49616957..49635747,92	K562	blood:

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

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

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

rs_ID	r²[population]
rs10047512	1.00[AMR][1000 genomes]
rs10047588	1.00[AMR][1000 genomes]
rs1109811	1.00[AMR][1000 genomes]
rs11168925	1.00[AMR][1000 genomes]
rs11168927	1.00[AMR][1000 genomes]
rs11168928	1.00[AMR][1000 genomes]
rs11168931	1.00[AMR][1000 genomes]
rs11168938	1.00[AMR][1000 genomes]
rs11168939	1.00[AMR][1000 genomes]
rs11168940	1.00[AMR][1000 genomes]
rs11168942	1.00[AMR][1000 genomes]
rs12296231	1.00[AMR][1000 genomes]
rs12296536	1.00[AMR][1000 genomes]
rs12297433	1.00[AMR][1000 genomes]
rs12300386	1.00[AMR][1000 genomes]
rs12300998	1.00[AMR][1000 genomes]
rs12304259	1.00[AMR][1000 genomes]
rs12304483	1.00[AMR][1000 genomes]
rs12304746	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12309028	1.00[AMR][1000 genomes]
rs12314967	1.00[AMR][1000 genomes]
rs12318666	1.00[AMR][1000 genomes]
rs12322876	1.00[AMR][1000 genomes]
rs28758893	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:36 , 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	chr12:49617800-49621400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:49617800-49621400	Weak transcription	Brain Angular Gyrus	brain
12	chr12:49617800-49621400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:49617800-49621400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr12:49618000-49621400	Weak transcription	Brain Anterior Caudate	brain
15	chr12:49618400-49621400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:49619200-49624000	Weak transcription	Primary B cells from cord blood	blood
17	chr12:49619800-49621400	Weak transcription	Brain Substantia Nigra	brain
18	chr12:49619800-49624600	Weak transcription	HSMM	muscle
19	chr12:49619800-49627200	Weak transcription	Lung	lung
20	chr12:49620000-49622400	Weak transcription	K562	blood
21	chr12:49620000-49623400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr12:49620000-49624000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr12:49620000-49626000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:49620200-49623200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr12:49620200-49623400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr12:49620600-49621400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:49620600-49622000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr12:49620600-49622000	Enhancers	HSMMtube	muscle
29	chr12:49620800-49621600	Enhancers	Fetal Brain Male	brain
30	chr12:49620800-49622200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:49621000-49621400	Enhancers	Fetal Brain Female	brain
32	chr12:49621000-49621600	Enhancers	Brain Germinal Matrix	brain
33	chr12:49621000-49621800	Enhancers	Fetal Muscle Leg	muscle
34	chr12:49621000-49622000	Enhancers	Brain Hippocampus Middle	brain
35	chr12:49621200-49622000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:49621200-49625400	Weak transcription	Fetal Muscle Trunk	muscle

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