Variant report

Variant	rs12255
Chromosome Location	chr12:123350204-123350205
allele	C/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123349459..123352177-chr12:123465556..123468107,2	K562	blood:
2	chr12:123350122..123350678-chr12:123722363..123722904,2	MCF-7	breast:
3	chr12:123348260..123351060-chr12:123715794..123718322,2	K562	blood:
4	chr12:123349944..123351476-chr12:123367250..123369233,2	K562	blood:
5	chr12:123318351..123322726-chr12:123344658..123350717,8	MCF-7	breast:
6	chr12:123341988..123344732-chr12:123349863..123352592,2	MCF-7	breast:
7	chr12:123348287..123350765-chr12:123373068..123375043,2	MCF-7	breast:
8	chr12:123349951..123350563-chr12:123436556..123437356,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000182196	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000139722	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000051825	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10744422	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10744434	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773627	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10773657	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10847826	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10847869	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11060064	0.81[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap]
rs11060065	0.81[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap]
rs12298151	0.90[ASN][1000 genomes]
rs12313006	0.86[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs12314544	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs12426809	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1532835	0.92[EUR][1000 genomes]
rs1587856	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1696326	0.86[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs1799618	0.86[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs2061098	0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2061101	0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2135014	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs2271049	0.89[ASN][1000 genomes]
rs2271050	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs2271051	0.85[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs2292132	0.90[EUR][1000 genomes]
rs2292134	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes]
rs2292135	0.92[EUR][1000 genomes]
rs2292136	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2292138	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292139	0.92[ASN][1000 genomes]
rs2343108	0.91[EUR][1000 genomes]
rs2343109	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2343685	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2880678	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3817094	0.90[EUR][1000 genomes]
rs3825143	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3852536	0.92[EUR][1000 genomes]
rs3852537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4759355	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4759381	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4759382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4759386	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4759387	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4759389	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4759392	0.80[AMR][1000 genomes]
rs4759393	0.83[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap]
rs59192320	0.92[ASN][1000 genomes]
rs6489245	1.00[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap]
rs6489247	0.83[CEU][hapmap]
rs7138398	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7139055	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs7294991	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes]
rs7309225	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.80[TSI][hapmap]
rs7957643	0.81[CEU][hapmap]
rs7959441	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7972447	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7980541	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs839360	0.86[CHB][hapmap]
rs897385	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs897386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs897391	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs897393	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs921808	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs936083	0.83[CEU][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs937766	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	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
3	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS 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	47 gene(s)	inside rSNPs	diseases
5	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
6	nsv899574	chr12:123316566-123360151	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv899575	chr12:123326374-123360151	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12255	ACADS	cis	parietal	SCAN
rs12255	CCDC62	cis	cerebellum	SCAN
rs12255	VPS37B	cis	multi-tissue	Pritchard
rs12255	HIP1R	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123322800-123353000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:123323200-123352000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr12:123324600-123352800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:123324800-123351600	Weak transcription	Small Intestine	intestine
5	chr12:123327400-123352600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:123327600-123353400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:123329200-123355000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:123332600-123355600	Strong transcription	Thymus	Thymus
9	chr12:123337400-123356200	Weak transcription	Fetal Kidney	kidney
10	chr12:123337600-123351000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:123337600-123351400	Weak transcription	HSMMtube	muscle
12	chr12:123337800-123351600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:123338400-123350400	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr12:123338400-123351000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:123338800-123354200	Strong transcription	Brain Germinal Matrix	brain
16	chr12:123339000-123353200	Weak transcription	K562	blood
17	chr12:123339200-123354200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr12:123339600-123354200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr12:123339600-123355000	Strong transcription	Fetal Brain Female	brain
20	chr12:123341200-123350800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr12:123341200-123352200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:123344400-123350600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:123344400-123351600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr12:123344400-123355000	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr12:123344600-123350600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:123344600-123350800	Weak transcription	Aorta	Aorta
27	chr12:123344600-123353000	Enhancers	Liver	Liver
28	chr12:123344800-123355200	Weak transcription	Hela-S3	cervix
29	chr12:123345000-123353600	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr12:123345200-123352600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr12:123345200-123354000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:123345200-123355400	Weak transcription	Fetal Brain Male	brain
33	chr12:123345400-123350400	Weak transcription	Psoas Muscle	Psoas
34	chr12:123345400-123352200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:123345400-123353800	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr12:123345400-123354400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:123345600-123351200	Weak transcription	GM12878-XiMat	blood
38	chr12:123345600-123355400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:123345800-123352800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:123345800-123354000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:123346200-123352800	Weak transcription	Colon Smooth Muscle	Colon
42	chr12:123346400-123352400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:123346600-123350600	Weak transcription	HUVEC	blood vessel
44	chr12:123346800-123351400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr12:123347000-123351200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:123347200-123354800	Strong transcription	Fetal Stomach	stomach
47	chr12:123347400-123355000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr12:123347600-123350800	Genic enhancers	Fetal Thymus	thymus
49	chr12:123347600-123353800	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr12:123347600-123354200	Strong transcription	Primary monocytes fromperipheralblood	blood

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