Variant report

Variant	rs12320259
Chromosome Location	chr12:12300169-12300170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10400407	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10466849	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs10845488	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11054703	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12313200	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]
rs12314259	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12422312	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs12425946	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs34143386	0.89[EUR][1000 genomes]
rs6488506	0.93[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs718403	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7301012	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308712	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7963810	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12320259	RIMKLB	cis	cerebellum	SCAN
rs12320259	FAM90A1	cis	cerebellum	SCAN

Chromatin state (count:106 , 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	chr12:12262400-12335600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:12263800-12314600	Weak transcription	Esophagus	oesophagus
4	chr12:12264000-12301400	Weak transcription	Right Ventricle	heart
5	chr12:12264400-12311400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:12265600-12303400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:12267800-12301600	Weak transcription	NHLF	lung
8	chr12:12268800-12301600	Weak transcription	Brain Substantia Nigra	brain
9	chr12:12269600-12343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:12271000-12301600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr12:12271400-12306600	Weak transcription	Small Intestine	intestine
12	chr12:12272200-12344600	Weak transcription	Primary B cells from cord blood	blood
13	chr12:12272400-12325200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr12:12272600-12305000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:12273600-12301600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr12:12274600-12313600	Weak transcription	Colonic Mucosa	Colon
17	chr12:12275000-12303400	Weak transcription	GM12878-XiMat	blood
18	chr12:12277400-12306800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:12277600-12311600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:12278200-12301400	Weak transcription	Placenta	Placenta
21	chr12:12278200-12310600	Weak transcription	Hela-S3	cervix
22	chr12:12279600-12301400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:12279800-12303600	Weak transcription	Fetal Brain Male	brain
24	chr12:12279800-12311000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:12279800-12311000	Weak transcription	HMEC	breast
26	chr12:12279800-12311600	Weak transcription	Dnd41	blood
27	chr12:12279800-12313800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr12:12279800-12342800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr12:12280000-12301600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr12:12280000-12301600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:12280000-12302600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr12:12280000-12303400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr12:12280600-12301600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr12:12281400-12301600	Weak transcription	Left Ventricle	heart
35	chr12:12281800-12335600	Weak transcription	Psoas Muscle	Psoas
36	chr12:12283200-12303400	Weak transcription	HSMM	muscle
37	chr12:12283400-12309200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:12284000-12301600	Weak transcription	NHDF-Ad	bronchial
39	chr12:12284800-12304600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:12285000-12301600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:12285000-12301600	Weak transcription	Aorta	Aorta
42	chr12:12285000-12309800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:12285000-12311400	Weak transcription	Pancreas	Pancrea
44	chr12:12285600-12315000	Weak transcription	Fetal Heart	heart
45	chr12:12287400-12318200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:12288200-12301600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr12:12288200-12301600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:12288200-12301600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr12:12288200-12310600	Weak transcription	Colon Smooth Muscle	Colon
50	chr12:12288200-12342800	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links