Variant report

Variant	rs12310205
Chromosome Location	chr12:123599725-123599726
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr12:123599722-123600663	IMR90	lung:	n/a	chr12:123600484-123600493

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123597677..123600543-chr12:123624922..123626506,2	K562	blood:
2	chr12:123598890..123601650-chr12:123601866..123605162,4	K562	blood:
3	chr12:123597462..123600001-chr12:123600120..123602268,2	MCF-7	breast:
4	chr12:123574271..123575945-chr12:123599295..123601794,2	MCF-7	breast:
5	chr12:123599616..123601650-chr12:123601866..123604392,2	K562	blood:
6	chr12:123583370..123585384-chr12:123598007..123600028,3	K562	blood:
7	chr12:123594524..123596302-chr12:123598140..123599856,2	MCF-7	breast:

No data

Variant related genes	Relation type
PITPNM2	TF binding region
ENSG00000090975	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11061612	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11834598	0.83[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12313619	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12317784	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12318090	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6489253	0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6650207	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7307833	0.83[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7953918	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv870326	chr12:123585990-123719323	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12310205	SBNO1	cis	multi-tissue	Pritchard

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123561600-123604000	Genic enhancers	Fetal Thymus	thymus
2	chr12:123571200-123600000	Genic enhancers	Thymus	Thymus
3	chr12:123590000-123603800	Enhancers	Left Ventricle	heart
4	chr12:123592000-123599800	Weak transcription	HMEC	breast
5	chr12:123592200-123600200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr12:123592200-123601000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:123592400-123601000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:123592800-123611200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:123594000-123602200	Enhancers	Brain Cingulate Gyrus	brain
10	chr12:123594600-123607200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:123594600-123634000	Weak transcription	Brain Germinal Matrix	brain
12	chr12:123595200-123599800	Weak transcription	Fetal Intestine Small	intestine
13	chr12:123595200-123600000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:123595200-123610800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:123595600-123600400	Enhancers	Fetal Heart	heart
16	chr12:123595600-123601200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr12:123596600-123604800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:123597000-123600200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr12:123597400-123608200	Enhancers	Primary B cells from peripheral blood	blood
20	chr12:123597800-123601600	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr12:123597800-123602000	Enhancers	Brain Angular Gyrus	brain
22	chr12:123597800-123602600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr12:123597800-123610800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:123598000-123600200	Weak transcription	A549	lung
25	chr12:123598000-123601200	Enhancers	Brain Hippocampus Middle	brain
26	chr12:123598000-123603400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:123598000-123608400	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr12:123598200-123600000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:123598200-123604800	Enhancers	Primary T cells from cord blood	blood
30	chr12:123598400-123600200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:123598400-123600600	Enhancers	HUVEC	blood vessel
32	chr12:123598400-123601000	Enhancers	Placenta Amnion	Placenta Amnion
33	chr12:123598600-123599800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:123598600-123600000	Enhancers	Brain Substantia Nigra	brain
35	chr12:123598600-123600000	Enhancers	Fetal Lung	lung
36	chr12:123598600-123602000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr12:123598600-123602000	Enhancers	Right Atrium	heart
38	chr12:123598600-123606400	Weak transcription	HepG2	liver
39	chr12:123598800-123600600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:123598800-123600800	Enhancers	Fetal Muscle Leg	muscle
41	chr12:123598800-123600800	Enhancers	NHEK	skin
42	chr12:123598800-123601000	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr12:123598800-123601400	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr12:123598800-123601400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:123598800-123601400	Enhancers	Fetal Stomach	stomach
46	chr12:123598800-123601400	Enhancers	Psoas Muscle	Psoas
47	chr12:123598800-123601800	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr12:123598800-123602800	Enhancers	Primary T cells fromperipheralblood	blood
49	chr12:123598800-123603600	Enhancers	Right Ventricle	heart
50	chr12:123598800-123603800	Enhancers	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links