Variant report

Variant	rs12133492
Chromosome Location	chr1:153832165-153832166
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153825600..153828097-chr1:153830690..153832423,2	K562	blood:
2	chr1:153825064..153829041-chr1:153831556..153834384,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223599	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10127484	0.85[EUR][1000 genomes]
rs10908525	0.84[EUR][1000 genomes]
rs10908526	0.84[EUR][1000 genomes]
rs11264573	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11264621	0.84[EUR][1000 genomes]
rs1127091	0.87[EUR][1000 genomes]
rs1139620	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800001	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12120118	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124424	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129468	0.93[ASN][1000 genomes]
rs12130611	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133923	0.86[EUR][1000 genomes]
rs12142639	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12142733	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12738361	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252508	0.82[EUR][1000 genomes]
rs35711150	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4276953	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4341393	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4370789	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4451582	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4540690	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4581307	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4596938	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803655	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427300	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427306	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668066	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677794	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6690619	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6700115	0.87[EUR][1000 genomes]
rs72694233	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7414227	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7415004	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7522030	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7554469	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9426935	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9426938	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427232	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427233	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
6	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
7	esv1825076	chr1:153779296-153843413	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153791800-153845600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:153800800-153832600	Weak transcription	Aorta	Aorta
3	chr1:153800800-153832800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:153800800-153835600	Weak transcription	Ovary	ovary
5	chr1:153800800-153850800	Weak transcription	A549	lung
6	chr1:153800800-153852800	Weak transcription	Fetal Brain Female	brain
7	chr1:153800800-153852800	Weak transcription	Placenta	Placenta
8	chr1:153800800-153852800	Weak transcription	Left Ventricle	heart
9	chr1:153800800-153853000	Weak transcription	Fetal Kidney	kidney
10	chr1:153801600-153845800	Weak transcription	Lung	lung
11	chr1:153801800-153836600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:153806200-153845400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:153814800-153835200	Weak transcription	Osteobl	bone
14	chr1:153814800-153839000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:153814800-153848000	Weak transcription	Fetal Heart	heart
16	chr1:153814800-153853400	Weak transcription	HSMMtube	muscle
17	chr1:153816000-153844000	Weak transcription	Right Ventricle	heart
18	chr1:153816600-153836200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:153816800-153834600	Weak transcription	Brain Angular Gyrus	brain
20	chr1:153821400-153832800	Weak transcription	Gastric	stomach
21	chr1:153821600-153839800	Weak transcription	Small Intestine	intestine
22	chr1:153822000-153836000	Weak transcription	Liver	Liver
23	chr1:153822000-153838600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:153822600-153839000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:153822600-153839400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:153822800-153853400	Weak transcription	HMEC	breast
27	chr1:153822800-153854200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:153823200-153833600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:153823600-153845400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:153823800-153833600	Strong transcription	Dnd41	blood
31	chr1:153824000-153843600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:153825000-153840200	Weak transcription	NHEK	skin
33	chr1:153825200-153836600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:153825200-153838800	Weak transcription	Brain Hippocampus Middle	brain
35	chr1:153825400-153836600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:153825600-153833200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:153825600-153833200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:153825600-153838800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:153825800-153836200	Weak transcription	Pancreas	Pancrea
40	chr1:153825800-153836600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr1:153825800-153836600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:153825800-153838800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:153825800-153838800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:153825800-153838800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:153825800-153838800	Weak transcription	Adipose Nuclei	Adipose
46	chr1:153825800-153838800	Weak transcription	Brain Anterior Caudate	brain
47	chr1:153825800-153838800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr1:153825800-153839000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr1:153825800-153842000	Weak transcription	Fetal Intestine Large	intestine
50	chr1:153825800-153845800	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links