Variant report

Variant	rs12313200
Chromosome Location	chr12:12284590-12284591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10400407	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10466849	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs10845488	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11054703	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12314259	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12320259	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422312	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs12425946	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs34143386	0.90[EUR][1000 genomes]
rs6488506	0.93[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs718403	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7301012	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308712	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7963810	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12313200	FAM90A1	cis	cerebellum	SCAN
rs12313200	RIMKLB	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12261600-12301400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr12:12261800-12288000	Weak transcription	Gastric	stomach
3	chr12:12262400-12335600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:12262800-12284800	Weak transcription	Aorta	Aorta
5	chr12:12263800-12314600	Weak transcription	Esophagus	oesophagus
6	chr12:12264000-12301400	Weak transcription	Right Ventricle	heart
7	chr12:12264200-12284600	Weak transcription	Pancreas	Pancrea
8	chr12:12264400-12284800	Weak transcription	Lung	lung
9	chr12:12264400-12311400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:12265600-12303400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:12267800-12301600	Weak transcription	NHLF	lung
12	chr12:12268800-12301600	Weak transcription	Brain Substantia Nigra	brain
13	chr12:12269600-12343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:12270600-12284800	Weak transcription	Spleen	Spleen
15	chr12:12271000-12301600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:12271400-12286600	Strong transcription	Liver	Liver
17	chr12:12271400-12306600	Weak transcription	Small Intestine	intestine
18	chr12:12271600-12288400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:12271600-12294200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr12:12271800-12285000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:12271800-12285600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:12271800-12286400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:12272000-12285000	Strong transcription	Fetal Muscle Trunk	muscle
24	chr12:12272000-12286000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr12:12272200-12344600	Weak transcription	Primary B cells from cord blood	blood
26	chr12:12272400-12325200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:12272600-12285000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr12:12272600-12288400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:12272600-12305000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:12273400-12286600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:12273600-12301600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr12:12274200-12287800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:12274400-12284600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:12274600-12313600	Weak transcription	Colonic Mucosa	Colon
35	chr12:12275000-12303400	Weak transcription	GM12878-XiMat	blood
36	chr12:12276000-12285000	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr12:12276000-12285000	Strong transcription	Fetal Lung	lung
38	chr12:12276800-12290600	Weak transcription	HSMMtube	muscle
39	chr12:12277000-12284600	Weak transcription	Fetal Heart	heart
40	chr12:12277400-12306800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:12277600-12311600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr12:12278000-12287800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:12278200-12299200	Weak transcription	Brain Hippocampus Middle	brain
44	chr12:12278200-12301400	Weak transcription	Placenta	Placenta
45	chr12:12278200-12310600	Weak transcription	Hela-S3	cervix
46	chr12:12278600-12287800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr12:12279200-12294200	Weak transcription	Brain Angular Gyrus	brain
48	chr12:12279200-12299000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:12279600-12301400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr12:12279800-12284600	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links