Variant report

Variant	rs833484
Chromosome Location	chr12:49276718-49276719
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49246388..49252218-chr12:49276087..49280065,7	MCF-7	breast:
2	chr12:49275956..49279461-chr12:49283300..49286531,4	MCF-7	breast:
3	chr12:49253798..49263932-chr12:49272568..49285670,39	MCF-7	breast:
4	chr12:49253541..49263542-chr12:49271204..49284916,35	MCF-7	breast:
5	chr12:49275330..49277454-chr12:49281174..49283027,2	MCF-7	breast:
6	chr12:49275988..49277601-chr12:49279454..49281035,2	MCF-7	breast:
7	chr12:49270319..49273192-chr12:49274654..49277123,3	MCF-7	breast:
8	chr12:49244448..49248825-chr12:49273797..49278851,6	MCF-7	breast:
9	chr12:49275988..49277581-chr12:49412229..49413782,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000181929	Chromatin interaction
ENSG00000199394	Chromatin interaction
ENSG00000174243	Chromatin interaction
ENSG00000172602	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10783287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875883	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10875885	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs11168773	0.95[ASN][1000 genomes]
rs12369505	0.86[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2293449	0.82[CEU][hapmap]
rs2446985	0.94[ASN][1000 genomes]
rs2446986	0.90[ASN][1000 genomes]
rs2446987	0.92[ASN][1000 genomes]
rs2446999	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2447000	0.94[ASN][1000 genomes]
rs2447001	0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2453476	0.92[ASN][1000 genomes]
rs2926806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2934998	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3958875	0.91[ASN][1000 genomes]
rs4760647	0.95[ASN][1000 genomes]
rs833476	0.94[ASN][1000 genomes]
rs833478	0.92[ASN][1000 genomes]
rs833479	0.93[ASN][1000 genomes]
rs833483	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833839	0.93[CEU][hapmap]
rs833841	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469373	chr12:49256792-49285390	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
2	nsv558832	chr12:49256792-49285390	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
3	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs833484	CCDC65	cis	Thyroid	GTEx
rs833484	CCDC65	cis	Skin Sun Exposed Lower leg	GTEx
rs833484	CCDC65	cis	Esophagus Muscularis	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49271400-49278200	Enhancers	Liver	Liver
2	chr12:49273800-49276800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:49274000-49278800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:49275000-49278600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:49275200-49278200	Enhancers	Fetal Intestine Large	intestine
6	chr12:49275200-49278200	Enhancers	Fetal Intestine Small	intestine
7	chr12:49275400-49277800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:49275400-49278200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:49275600-49277000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:49275600-49277200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr12:49275600-49277200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:49275600-49277400	Enhancers	Placenta Amnion	Placenta Amnion
13	chr12:49275600-49277600	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr12:49275600-49277800	Enhancers	Placenta	Placenta
15	chr12:49275600-49278000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr12:49275600-49278000	Enhancers	Fetal Lung	lung
17	chr12:49275600-49278000	Enhancers	Lung	lung
18	chr12:49275600-49278000	Enhancers	Pancreas	Pancrea
19	chr12:49275600-49278200	Flanking Active TSS	A549	lung
20	chr12:49275800-49277000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr12:49275800-49277000	Flanking Active TSS	HUVEC	blood vessel
22	chr12:49275800-49277200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr12:49275800-49277200	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr12:49275800-49278000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr12:49275800-49278000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:49275800-49278000	Enhancers	Duodenum Mucosa	Duodenum
27	chr12:49275800-49278200	Enhancers	H1 Cell Line	embryonic stem cell
28	chr12:49275800-49278200	Enhancers	Brain Angular Gyrus	brain
29	chr12:49275800-49278200	Enhancers	Fetal Brain Male	brain
30	chr12:49275800-49278200	Enhancers	K562	blood
31	chr12:49276000-49276800	Weak transcription	Gastric	stomach
32	chr12:49276000-49277400	Enhancers	Brain Cingulate Gyrus	brain
33	chr12:49276000-49277400	Enhancers	Brain Germinal Matrix	brain
34	chr12:49276000-49277600	Enhancers	Fetal Muscle Trunk	muscle
35	chr12:49276000-49277800	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr12:49276000-49277800	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr12:49276000-49278000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:49276000-49278000	Enhancers	Fetal Brain Female	brain
39	chr12:49276000-49278200	Bivalent Enhancer	Fetal Stomach	stomach
40	chr12:49276200-49276800	Weak transcription	Brain Anterior Caudate	brain
41	chr12:49276200-49277000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
42	chr12:49276200-49277400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:49276200-49278000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:49276200-49278400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:49276400-49276800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:49276400-49277000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:49276400-49277400	Bivalent Enhancer	NHLF	lung
48	chr12:49276400-49277800	Enhancers	Right Atrium	heart
49	chr12:49276400-49278000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:49276400-49278200	Enhancers	H9 Cell Line	embryonic stem cell

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