Variant report

Variant	rs12309341
Chromosome Location	chr12:49459725-49459726
allele	G/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	chr12:49446392..49469923-chr12:49518127..49527853,66	K562	blood:
2	chr12:49408338..49419708-chr12:49447252..49460551,38	K562	blood:
3	chr12:49457901..49460694-chr12:49643033..49644659,2	K562	blood:
4	chr12:49456178..49460565-chr12:49463551..49467043,4	MCF-7	breast:
5	chr12:49448896..49462070-chr12:49656751..49663992,28	K562	blood:
6	chr12:49451508..49465481-chr12:49521303..49528986,40	MCF-7	breast:
7	chr12:49457722..49460172-chr12:49483774..49486462,3	MCF-7	breast:
8	chr12:49440399..49469923-chr12:49518291..49528303,83	K562	blood:
9	chr12:49457724..49460435-chr12:49497636..49500149,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000167548	Chromatin interaction
ENSG00000167550	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000123416	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11168820	1.00[AMR][1000 genomes]
rs11168821	1.00[AMR][1000 genomes]
rs11168823	1.00[AMR][1000 genomes]
rs11168824	1.00[AMR][1000 genomes]
rs11168826	1.00[AMR][1000 genomes]
rs12303646	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12304391	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12310024	0.88[AFR][1000 genomes]
rs12315734	0.82[ASW][hapmap];1.00[AMR][1000 genomes]
rs13377622	1.00[ASW][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs13377924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13377927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3803024	1.00[MEX][hapmap]
rs4018512	1.00[ASW][hapmap];1.00[AMR][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	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12309341	PRKAG1	cis	lymphoblastoid	seeQTL
rs12309341	TUBA1A	cis	lymphoblastoid	seeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49455200-49461800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:49455200-49462800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr12:49455200-49462800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:49455400-49460200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:49455400-49461800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:49455400-49461800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:49455400-49462600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:49455400-49462600	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr12:49455400-49462600	Weak transcription	Primary T cells from cord blood	blood
10	chr12:49455400-49462600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:49455400-49462600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr12:49455400-49462600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:49455400-49462600	Weak transcription	Brain Hippocampus Middle	brain
14	chr12:49455400-49462800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:49455400-49462800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr12:49455400-49462800	Weak transcription	Fetal Lung	lung
17	chr12:49455400-49462800	Weak transcription	Right Ventricle	heart
18	chr12:49455400-49462800	Weak transcription	HSMM	muscle
19	chr12:49455400-49463000	Weak transcription	Lung	lung
20	chr12:49455400-49463200	Weak transcription	Aorta	Aorta
21	chr12:49455600-49459800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:49455600-49460200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:49455600-49461800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr12:49455600-49462400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:49455600-49462400	Weak transcription	GM12878-XiMat	blood
26	chr12:49455600-49462600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:49455600-49462600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:49455600-49462600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr12:49455600-49462600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr12:49455600-49462600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:49455600-49462600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:49455600-49462600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:49455600-49462600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr12:49455600-49462600	Weak transcription	Fetal Thymus	thymus
35	chr12:49455600-49462600	Weak transcription	HMEC	breast
36	chr12:49455600-49462600	Weak transcription	HUVEC	blood vessel
37	chr12:49455600-49462600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr12:49455600-49462600	Weak transcription	NH-A	brain
39	chr12:49455600-49462800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:49455600-49462800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:49455600-49462800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:49455600-49462800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr12:49455600-49462800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:49455600-49462800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:49455600-49462800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:49455600-49462800	Weak transcription	Brain Substantia Nigra	brain
47	chr12:49455600-49462800	Weak transcription	Fetal Kidney	kidney
48	chr12:49455600-49462800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr12:49455600-49462800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:49455600-49463000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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