Variant report

Variant	rs12223858
Chromosome Location	chr11:18495915-18495916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10219166	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10832938	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10832942	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10832943	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10832945	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11024670	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024671	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11024674	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11024675	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11024676	0.85[EUR][1000 genomes]
rs11024678	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11024679	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11024683	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11024685	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024689	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11024695	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11024696	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11024706	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11024716	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11024723	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11024724	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12049851	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12049909	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12049912	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12222210	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12223887	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12225461	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12225463	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12290527	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12418726	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12419360	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12419592	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12420702	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12420882	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12421881	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12574333	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12575390	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12577874	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12803251	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16914838	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16935504	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2271080	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2279900	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2305166	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28607050	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3781639	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55964013	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55999230	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56097703	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56151250	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56151849	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56411332	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59032896	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61882885	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61882887	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61882903	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882904	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61884677	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7108487	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7109314	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7130163	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72871737	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72876745	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7950602	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9633899	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS 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	156 gene(s)	inside rSNPs	diseases
2	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers 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	144 gene(s)	inside rSNPs	diseases
3	nsv1047049	chr11:18359702-18520008	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv540955	chr11:18359702-18520008	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv897027	chr11:18435700-18499416	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1038015	chr11:18435855-18558211	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1042155	chr11:18435855-18697576	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	72 gene(s)	inside rSNPs	diseases
8	nsv467719	chr11:18447611-18542227	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	nsv553634	chr11:18447611-18542227	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12223858	TSG101	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18477600-18498400	Weak transcription	Spleen	Spleen
2	chr11:18477800-18498000	Weak transcription	Fetal Brain Female	brain
3	chr11:18478200-18497600	Weak transcription	Right Ventricle	heart
4	chr11:18479800-18496200	Weak transcription	Fetal Intestine Large	intestine
5	chr11:18480000-18499400	Weak transcription	HSMMtube	muscle
6	chr11:18483600-18498400	Weak transcription	Aorta	Aorta
7	chr11:18483600-18526200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr11:18485800-18497000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr11:18485800-18498200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr11:18486200-18496600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:18486600-18496200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:18487600-18497800	Weak transcription	Gastric	stomach
13	chr11:18488200-18496600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr11:18488400-18501200	Weak transcription	Esophagus	oesophagus
15	chr11:18488400-18501400	Weak transcription	HepG2	liver
16	chr11:18488600-18497800	Weak transcription	Ovary	ovary
17	chr11:18488600-18498400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr11:18488800-18496800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:18489000-18496200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr11:18489000-18497800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr11:18489000-18497800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr11:18489200-18496200	Weak transcription	Fetal Muscle Leg	muscle
23	chr11:18489400-18496600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr11:18489400-18498400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr11:18489800-18496200	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr11:18489800-18500600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr11:18490000-18496000	Weak transcription	Fetal Stomach	stomach
28	chr11:18490200-18496600	Weak transcription	Adipose Nuclei	Adipose
29	chr11:18490200-18497000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr11:18490400-18496400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr11:18490400-18496400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr11:18490400-18496600	Weak transcription	Primary T cells from cord blood	blood
33	chr11:18490400-18496600	Weak transcription	Fetal Lung	lung
34	chr11:18490400-18497000	Weak transcription	Colon Smooth Muscle	Colon
35	chr11:18490400-18500000	Weak transcription	HUVEC	blood vessel
36	chr11:18490800-18497000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr11:18491000-18499200	Weak transcription	GM12878-XiMat	blood
38	chr11:18491200-18496000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr11:18491400-18496400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr11:18491600-18496400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr11:18491600-18498000	Weak transcription	Placenta	Placenta
42	chr11:18491800-18496200	Weak transcription	Fetal Thymus	thymus
43	chr11:18491800-18498400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr11:18492000-18496400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr11:18492000-18496800	Weak transcription	A549	lung
46	chr11:18492000-18496800	Weak transcription	HSMM	muscle
47	chr11:18492000-18497000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr11:18492200-18496200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr11:18492200-18496400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:18492200-18496400	Weak transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links