Variant report

Variant	rs11611288
Chromosome Location	chr12:50911101-50911102
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50901773..50903761-chr12:50910341..50913326,3	MCF-7	breast:
2	chr12:50909307..50911396-chr12:50923747..50926654,2	K562	blood:
3	chr12:50906998..50909995-chr12:50910292..50911988,2	MCF-7	breast:
4	chr12:50898826..50901477-chr12:50910809..50913079,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066084	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10747586	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783366	0.89[CEU][hapmap]
rs10783367	0.89[EUR][1000 genomes]
rs10783377	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783380	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876041	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs10876044	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs10876046	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1109726	1.00[ASN][1000 genomes]
rs11609231	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11609506	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11614911	0.88[EUR][1000 genomes]
rs11832315	1.00[CEU][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821270	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1521516	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs2250751	1.00[ASN][1000 genomes]
rs2250752	1.00[ASN][1000 genomes]
rs2251024	1.00[ASN][1000 genomes]
rs2251603	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252589	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684889	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2684898	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684900	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684901	1.00[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700479	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700480	1.00[CEU][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700482	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2700485	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2731434	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2731439	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2731440	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731442	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731443	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs4768885	0.87[EUR][1000 genomes]
rs4768886	0.87[EUR][1000 genomes]
rs55939211	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56089074	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56104942	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66597435	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66644594	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67701624	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs68171620	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131795	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135837	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7300979	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305655	1.00[CEU][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307815	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957060	0.85[EUR][1000 genomes]
rs7960015	1.00[ASN][1000 genomes]
rs7968440	1.00[ASN][1000 genomes]
rs7977690	1.00[ASN][1000 genomes]
rs7979165	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1820967	chr12:50856613-51002088	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11611288	CERS5	cis	Nerve Tibial	GTEx
rs11611288	KIAA1463	cis	multi-tissue	Pritchard
rs11611288	DIP2B	cis	multi-tissue	Pritchard
rs11611288	LASS5	cis	multi-tissue	Pritchard

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50900000-50911800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:50900000-50925400	Weak transcription	Esophagus	oesophagus
3	chr12:50900200-50911200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:50900600-50916400	Enhancers	Primary B cells from peripheral blood	blood
5	chr12:50900600-50932000	Weak transcription	Fetal Kidney	kidney
6	chr12:50900800-50911200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:50901400-50925600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:50901600-50915600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:50902200-50911200	Weak transcription	Dnd41	blood
10	chr12:50902600-50911200	Weak transcription	Fetal Brain Male	brain
11	chr12:50902800-50912000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr12:50903200-50911200	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:50903400-50925800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:50903600-50911200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr12:50903600-50911400	Weak transcription	Psoas Muscle	Psoas
16	chr12:50903600-50922800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr12:50904200-50911200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:50904400-50911200	Weak transcription	A549	lung
19	chr12:50904400-50911400	Weak transcription	Fetal Intestine Small	intestine
20	chr12:50906400-50911200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:50906400-50915600	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr12:50906400-50916400	Enhancers	Primary T cells fromperipheralblood	blood
23	chr12:50906800-50911200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:50907000-50911800	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr12:50907200-50911200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:50907200-50911600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:50907200-50915200	Enhancers	HepG2	liver
28	chr12:50907400-50911200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:50907400-50911200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr12:50907400-50911400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:50907400-50911400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:50907400-50917800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:50907800-50912800	Enhancers	Spleen	Spleen
34	chr12:50907800-50913200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr12:50908200-50911800	Enhancers	Fetal Thymus	thymus
36	chr12:50908200-50912600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:50908600-50911200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr12:50908800-50915600	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr12:50909000-50911200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr12:50909000-50911200	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr12:50909000-50911200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr12:50909000-50911200	Weak transcription	Stomach Mucosa	stomach
43	chr12:50909000-50911400	Weak transcription	Right Atrium	heart
44	chr12:50909000-50914000	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr12:50909000-50915400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr12:50909000-50919800	Weak transcription	Right Ventricle	heart
47	chr12:50909000-50925400	Weak transcription	Lung	lung
48	chr12:50909200-50911200	Enhancers	Primary hematopoietic stem cells	blood
49	chr12:50909200-50911200	Weak transcription	Liver	Liver
50	chr12:50909400-50911200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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