Variant report

Variant	rs12222154
Chromosome Location	chr11:18552899-18552900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr11:18552823-18553016	HepG2	liver:	n/a	n/a
2	POLR2A	chr11:18552658-18553134	K562	blood:	n/a	n/a
3	CEBPB	chr11:18552382-18553040	Hela-S3	cervix:	n/a	n/a
4	FOS	chr11:18552374-18552951	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr11:18552373-18552920	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:18551902..18554921-chr11:18560952..18564096,3	K562	blood:
2	chr11:18546489..18551340-chr11:18552893..18563258,14	MCF-7	breast:
3	chr11:18552647..18555345-chr20:55842668..55844786,2	MCF-7	breast:
4	chr11:18551088..18554076-chr11:18654231..18656218,2	K562	blood:

Variant related genes	Relation type
TSG101	TF binding region
ENSG00000179119	Chromatin interaction
ENSG00000074319	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10500835	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11024669	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11024677	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11024688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11024693	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11024706	0.90[TSI][hapmap]
rs11024714	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11024715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11024719	1.00[YRI][hapmap]
rs11024725	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024726	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024727	1.00[JPT][hapmap];0.90[TSI][hapmap]
rs12289223	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12418726	0.90[TSI][hapmap]
rs12421394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12574333	0.86[TSI][hapmap]
rs16935541	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16935559	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16935575	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1979051	0.94[JPT][hapmap]
rs1983124	0.95[JPT][hapmap]
rs2279900	0.86[TSI][hapmap]
rs2279902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2291751	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2292179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2305166	0.90[TSI][hapmap]
rs3781640	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4436523	0.95[JPT][hapmap];0.95[TSI][hapmap]
rs55969503	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61882886	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61884673	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61884715	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61884716	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61884723	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61884724	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61886140	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61886141	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6416020	1.00[JPT][hapmap];0.86[TSI][hapmap]
rs7950602	0.90[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	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
5	nsv1046886	chr11:18547568-18781448	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv540956	chr11:18547568-18781448	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12222154	UEVLD	cis	cerebellum	SCAN
rs12222154	TSG101	cis	lymphoblastoid	seeQTL
rs12222154	NUCB2	cis	cerebellum	SCAN
rs12222154	LDHC	cis	parietal	SCAN
rs12222154	TSG101	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18549000-18576400	Weak transcription	Gastric	stomach
2	chr11:18549000-18577000	Weak transcription	Spleen	Spleen
3	chr11:18549200-18554200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr11:18549200-18568200	Weak transcription	Lung	lung
5	chr11:18549200-18577000	Weak transcription	Esophagus	oesophagus
6	chr11:18549200-18583400	Weak transcription	Small Intestine	intestine
7	chr11:18549200-18591400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr11:18549400-18553800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr11:18549400-18555200	Weak transcription	Aorta	Aorta
10	chr11:18549400-18576000	Weak transcription	Ovary	ovary
11	chr11:18549400-18576400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr11:18549400-18577000	Weak transcription	Colonic Mucosa	Colon
13	chr11:18549400-18579200	Weak transcription	Pancreas	Pancrea
14	chr11:18549400-18583400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr11:18549400-18594400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr11:18549600-18553600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr11:18549600-18555200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:18549600-18555200	Weak transcription	Adipose Nuclei	Adipose
19	chr11:18549600-18555200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr11:18549600-18555400	Weak transcription	Colon Smooth Muscle	Colon
21	chr11:18549600-18555400	Weak transcription	HSMMtube	muscle
22	chr11:18549600-18557800	Weak transcription	Brain Hippocampus Middle	brain
23	chr11:18549600-18565000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr11:18549600-18565400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr11:18549600-18565800	Weak transcription	Brain Germinal Matrix	brain
26	chr11:18549600-18567600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr11:18549600-18568000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr11:18549600-18568400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr11:18549600-18575000	Weak transcription	Fetal Brain Female	brain
30	chr11:18549600-18575200	Weak transcription	Fetal Kidney	kidney
31	chr11:18549600-18576400	Weak transcription	Brain Substantia Nigra	brain
32	chr11:18549600-18576600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr11:18549600-18576800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr11:18549600-18577200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr11:18549600-18577800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr11:18549600-18608600	Weak transcription	Fetal Heart	heart
37	chr11:18549600-18609000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr11:18549600-18609000	Weak transcription	Fetal Brain Male	brain
39	chr11:18549800-18553400	Weak transcription	NHDF-Ad	bronchial
40	chr11:18549800-18553600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr11:18549800-18553600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr11:18549800-18553600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr11:18549800-18553800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr11:18549800-18553800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr11:18549800-18554800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr11:18549800-18555000	Weak transcription	Fetal Intestine Large	intestine
47	chr11:18549800-18555200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr11:18549800-18555200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr11:18549800-18555200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:18549800-18555200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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