Variant report

Variant	rs12618133
Chromosome Location	chr2:96892134-96892135
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:96874338..96875886-chr2:96890330..96892404,2	MCF-7	breast:
2	chr2:96874731..96877568-chr2:96889613..96892545,3	K562	blood:
3	chr2:96873120..96874741-chr2:96890892..96892496,2	MCF-7	breast:
4	chr2:96857503..96859061-chr2:96889984..96892182,2	K562	blood:
5	chr2:96857561..96859544-chr2:96890682..96892503,2	K562	blood:

Variant related genes	Relation type
ENSG00000084090	Chromatin interaction
ENSG00000204685	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11551400	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs11886999	0.80[CEU][hapmap]
rs12613263	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12617019	0.94[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2276650	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3852673	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4371393	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4592891	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4826	0.94[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57476471	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59082429	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59664047	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60409279	0.80[EUR][1000 genomes]
rs62153010	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62153011	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62153014	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62153018	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62153020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62153022	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62153029	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825854	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72825856	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72825864	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72825877	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579709	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7580178	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs997548	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][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	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription 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	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
9	nsv963665	chr2:96882253-96905611	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12618133	CIAO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96875000-96906200	Weak transcription	Esophagus	oesophagus
2	chr2:96875200-96905000	Weak transcription	Aorta	Aorta
3	chr2:96875600-96907000	Weak transcription	Fetal Thymus	thymus
4	chr2:96875800-96905800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:96876000-96896200	Weak transcription	Left Ventricle	heart
6	chr2:96876000-96902400	Weak transcription	Fetal Intestine Large	intestine
7	chr2:96876000-96904200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:96876000-96905800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:96876000-96906600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:96876000-96915200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:96876200-96893400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:96876200-96895800	Weak transcription	Lung	lung
13	chr2:96876200-96903200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:96876200-96903600	Weak transcription	Gastric	stomach
15	chr2:96876200-96905200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:96876200-96906000	Weak transcription	Osteobl	bone
17	chr2:96876200-96906600	Weak transcription	Brain Anterior Caudate	brain
18	chr2:96876200-96916000	Weak transcription	Dnd41	blood
19	chr2:96876200-96917800	Weak transcription	Brain Angular Gyrus	brain
20	chr2:96876600-96902600	Weak transcription	HepG2	liver
21	chr2:96877800-96916000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:96879600-96902400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr2:96879600-96903200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:96879600-96903200	Weak transcription	Fetal Stomach	stomach
25	chr2:96886000-96905400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:96886000-96905600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:96886400-96905000	Weak transcription	Fetal Heart	heart
28	chr2:96886800-96902200	Weak transcription	Fetal Intestine Small	intestine
29	chr2:96886800-96905000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:96887800-96905600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:96888000-96895600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:96888000-96905400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:96888400-96895800	Weak transcription	Psoas Muscle	Psoas
34	chr2:96888600-96896000	Weak transcription	Right Ventricle	heart
35	chr2:96889000-96903600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:96889600-96903400	Weak transcription	Primary T cells from cord blood	blood
37	chr2:96889600-96915800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr2:96890000-96892600	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr2:96891200-96916200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:96891400-96896000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr2:96891400-96902200	Weak transcription	Fetal Muscle Leg	muscle
42	chr2:96891400-96902800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:96891400-96916400	Weak transcription	HSMM	muscle
44	chr2:96891600-96896400	Weak transcription	K562	blood
45	chr2:96891600-96905600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:96891600-96906800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr2:96891800-96892200	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr2:96891800-96892800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr2:96891800-96899600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr2:96892000-96898800	Weak transcription	GM12878-XiMat	blood

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