Variant report

Variant	rs12133923
Chromosome Location	chr1:153773240-153773241
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153769239..153773675-chr1:153774397..153779052,9	K562	blood:
2	chr1:153767549..153769276-chr1:153772270..153774573,2	MCF-7	breast:
3	chr1:153771858..153774783-chr1:153961894..153965069,5	K562	blood:
4	chr1:153771018..153773380-chr1:153956396..153960280,3	MCF-7	breast:
5	chr1:153772217..153774028-chr1:153949824..153952504,2	K562	blood:
6	chr1:153770522..153773275-chr1:153961890..153963520,2	MCF-7	breast:
7	chr1:153771964..153774783-chr1:153963407..153965069,2	K562	blood:

Variant related genes	Relation type
ENSG00000143545	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000272654	Chromatin interaction
ENSG00000231827	Chromatin interaction
ENSG00000143543	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10127484	0.96[CEU][hapmap]
rs10908525	0.81[AFR][1000 genomes]
rs11264573	0.96[CEU][hapmap]
rs11264736	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs1127091	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1139620	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12120118	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12124424	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12130611	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12133492	0.86[EUR][1000 genomes]
rs12142733	0.88[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs12738361	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2252508	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs4276953	0.82[EUR][1000 genomes]
rs4341393	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4370789	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4451582	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4540690	0.86[EUR][1000 genomes]
rs4581307	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4596938	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs61803655	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs6427300	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6427306	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6661009	0.92[CEU][hapmap]
rs6664419	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6668066	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6677794	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6690619	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs6700115	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72694233	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7414227	0.96[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7415004	0.87[AFR][1000 genomes]
rs7522030	0.96[CEU][hapmap]
rs7532974	0.88[AFR][1000 genomes]
rs7532982	0.83[AFR][1000 genomes]
rs7554469	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9426935	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9426938	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9427220	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9427232	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9427233	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription 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	286 gene(s)	inside rSNPs	diseases
4	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv464039	chr1:153708906-153801098	Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription 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	45 gene(s)	inside rSNPs	diseases
6	nsv547941	chr1:153708906-153801098	Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv817392	chr1:153724807-153870005	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
9	nsv515962	chr1:153752139-153773429	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153757000-153779200	Weak transcription	Dnd41	blood
2	chr1:153762400-153776600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:153762600-153777600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr1:153762600-153777600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:153762600-153779600	Weak transcription	Gastric	stomach
6	chr1:153762600-153779600	Weak transcription	Pancreas	Pancrea
7	chr1:153763600-153776800	Weak transcription	Right Atrium	heart
8	chr1:153763600-153777800	Weak transcription	Fetal Intestine Large	intestine
9	chr1:153763600-153780000	Weak transcription	Aorta	Aorta
10	chr1:153763600-153780000	Weak transcription	Ovary	ovary
11	chr1:153763600-153780800	Weak transcription	Colonic Mucosa	Colon
12	chr1:153763800-153779400	Weak transcription	Brain Substantia Nigra	brain
13	chr1:153764000-153777000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr1:153764000-153777800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:153764000-153779600	Weak transcription	Brain Angular Gyrus	brain
16	chr1:153764400-153774000	Weak transcription	Osteobl	bone
17	chr1:153764400-153776000	Weak transcription	HSMMtube	muscle
18	chr1:153764400-153777600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:153764400-153777600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:153764400-153778200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr1:153764400-153779600	Weak transcription	Brain Anterior Caudate	brain
22	chr1:153764600-153776000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:153764600-153777600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:153764600-153777800	Weak transcription	NHLF	lung
25	chr1:153764800-153773400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:153764800-153776000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr1:153764800-153776200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:153765000-153775600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:153765400-153775000	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr1:153765400-153775000	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr1:153767000-153779400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr1:153767600-153782600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:153767800-153779600	Weak transcription	Fetal Lung	lung
34	chr1:153768000-153774000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:153768000-153775200	Weak transcription	Adipose Nuclei	Adipose
36	chr1:153768000-153777600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:153768000-153777800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:153768000-153779600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:153768000-153779600	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:153768000-153781400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:153768200-153777800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:153768200-153779200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:153768200-153779400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:153768200-153779600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:153768200-153779600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:153768400-153779200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr1:153768400-153779800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:153768800-153779000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:153769000-153776600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:153769200-153774200	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links