Variant report

Variant	rs12312134
Chromosome Location	chr12:48555303-48555304
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10082861	0.91[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10219623	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10219645	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10467101	0.83[CHB][hapmap]
rs10783234	0.83[ASN][1000 genomes]
rs10875724	0.86[JPT][hapmap]
rs10875725	0.93[JPT][hapmap]
rs10875732	0.92[JPT][hapmap]
rs10875745	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875746	0.94[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs10875747	0.90[ASN][1000 genomes]
rs10875748	0.90[ASN][1000 genomes]
rs10875750	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs10875756	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10875762	0.91[ASN][1000 genomes]
rs10875764	0.84[ASN][1000 genomes]
rs10875767	0.83[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs10875770	0.89[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10875772	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs10875793	0.85[JPT][hapmap]
rs11168357	0.86[JPT][hapmap]
rs11168369	0.93[JPT][hapmap]
rs11168371	0.93[JPT][hapmap]
rs11168403	0.93[JPT][hapmap]
rs11168413	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168414	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs11168415	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168416	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168418	1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.90[ASN][1000 genomes]
rs11168420	0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs11168421	0.91[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11168422	0.90[ASN][1000 genomes]
rs11168425	0.91[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168427	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs11168433	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11168450	0.94[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs11168459	0.89[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11168516	0.81[JPT][hapmap]
rs11558768	0.92[ASN][1000 genomes]
rs12297470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12304476	0.92[JPT][hapmap]
rs12305182	0.87[JPT][hapmap]
rs12305511	1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs12305647	0.89[ASN][1000 genomes]
rs12306290	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12306451	0.93[JPT][hapmap]
rs12310813	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17122666	0.94[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs17122812	0.84[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs1859445	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2012773	0.89[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs2079295	0.87[JPT][hapmap]
rs2107638	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2228500	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2269933	0.86[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2269935	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2269936	0.93[JPT][hapmap]
rs2279464	0.81[JPT][hapmap]
rs2286021	0.92[ASN][1000 genomes]
rs2634675	0.81[JPT][hapmap]
rs2732439	0.81[JPT][hapmap]
rs2732465	0.81[JPT][hapmap]
rs3185921	0.81[JPT][hapmap]
rs3751273	0.81[JPT][hapmap]
rs3782910	0.93[JPT][hapmap]
rs4760609	0.86[JPT][hapmap]
rs4760619	0.88[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4760622	1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.89[ASN][1000 genomes]
rs4760681	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[YRI][hapmap];0.92[ASN][1000 genomes]
rs4760684	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760687	0.91[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4760689	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4760690	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4760695	1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs4760696	0.94[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs4760697	0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs60106007	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61343568	0.81[ASN][1000 genomes]
rs61940962	0.81[ASN][1000 genomes]
rs6580659	0.85[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs7135779	0.89[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs719008	0.87[JPT][hapmap]
rs725454	0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs7299135	0.86[JPT][hapmap]
rs7299271	0.86[JPT][hapmap]
rs7485355	0.92[ASN][1000 genomes]
rs7486424	0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8804	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs886588	0.93[JPT][hapmap]
rs9634261	0.81[JPT][hapmap]
rs989144	0.93[JPT][hapmap]

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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12312134	RP1-228P16.1	cis	Artery Tibial	GTEx
rs12312134	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs12312134	RP1-228P16.1	cis	Thyroid	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48552000-48555800	Enhancers	Primary hematopoietic stem cells	blood
2	chr12:48552000-48556600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:48552000-48557800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:48552200-48556600	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr12:48552800-48556000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr12:48553800-48555400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:48553800-48555600	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr12:48553800-48555600	Enhancers	GM12878-XiMat	blood
9	chr12:48554000-48555600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:48554000-48555600	Enhancers	Fetal Heart	heart
11	chr12:48554000-48555800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr12:48554200-48555400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:48554600-48555400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr12:48554600-48556000	Enhancers	K562	blood
15	chr12:48554600-48556600	Enhancers	Psoas Muscle	Psoas
16	chr12:48554600-48557000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:48554800-48555600	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr12:48554800-48558200	Weak transcription	Brain Hippocampus Middle	brain
19	chr12:48555000-48556800	Weak transcription	Brain Anterior Caudate	brain
20	chr12:48555000-48558200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links