Variant report

Variant	rs11039166
Chromosome Location	chr11:47316691-47316692
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47296351..47298099-chr11:47314829..47317749,2	MCF-7	breast:
2	chr11:47315662..47317702-chr11:47325532..47327163,2	MCF-7	breast:
3	chr11:47314538..47316874-chr11:47373128..47374831,2	MCF-7	breast:
4	chr11:47315041..47318111-chr11:47327943..47330355,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110514	Chromatin interaction
ENSG00000134571	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10501321	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1052373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1055510	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10742799	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10742801	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10769252	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10838681	0.86[YRI][hapmap]
rs10838684	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10838687	0.83[CHB][hapmap];0.83[YRI][hapmap]
rs10838690	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10838691	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10838692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10838693	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039156	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11039167	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12575456	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1375688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1449627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2013867	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs2167079	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs2269434	0.94[CEU][hapmap];0.95[CHB][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2279239	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2291119	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2301216	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs326214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs326217	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs326222	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs35879051	0.88[EUR][1000 genomes]
rs3758669	0.83[EUR][1000 genomes]
rs3758672	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3758673	0.84[CEU][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3781621	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3781622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3816725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3847502	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4752822	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4752824	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752825	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4752980	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59663860	0.88[EUR][1000 genomes]
rs61896050	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6485746	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67871383	0.84[ASN][1000 genomes]
rs7109147	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7109203	0.80[EUR][1000 genomes]
rs7120118	0.90[CEU][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7120957	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7124955	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7127907	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129661	0.85[EUR][1000 genomes]
rs7395581	0.85[CEU][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs7940809	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs830085	0.90[CEU][hapmap];0.93[YRI][hapmap];0.83[EUR][1000 genomes]
rs901746	0.90[CEU][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11039166	NR1H3	cis	multi-tissue	Pritchard
rs11039166	PACSIN3	cis	Esophagus Mucosa	GTEx
rs11039166	ACP2	cis	Thyroid	GTEx
rs11039166	ACP2	cis	multi-tissue	Pritchard
rs11039166	ACP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47294600-47355200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr11:47295000-47323600	Strong transcription	Dnd41	blood
3	chr11:47295200-47319800	Strong transcription	Fetal Muscle Trunk	muscle
4	chr11:47295200-47320200	Strong transcription	Fetal Stomach	stomach
5	chr11:47295200-47321600	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr11:47295200-47323800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr11:47295200-47326800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:47295400-47318200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr11:47295400-47318800	Strong transcription	Thymus	Thymus
10	chr11:47295400-47319200	Strong transcription	Brain Cingulate Gyrus	brain
11	chr11:47295400-47319600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr11:47295400-47319600	Strong transcription	Fetal Brain Female	brain
13	chr11:47295400-47320800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr11:47295400-47321400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr11:47295400-47323800	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr11:47295400-47324800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:47295400-47324800	Strong transcription	Fetal Thymus	thymus
18	chr11:47295400-47340200	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr11:47295400-47341000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr11:47295400-47352600	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:47295600-47319600	Strong transcription	Fetal Muscle Leg	muscle
22	chr11:47295600-47320000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:47295600-47320200	Strong transcription	Fetal Intestine Large	intestine
24	chr11:47295600-47321200	Strong transcription	Brain Germinal Matrix	brain
25	chr11:47295600-47321800	Strong transcription	Primary B cells from peripheral blood	blood
26	chr11:47295600-47323800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr11:47295600-47323800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr11:47295600-47324000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:47295600-47324200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:47295600-47324200	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr11:47295600-47338800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr11:47295800-47319600	Strong transcription	Fetal Intestine Small	intestine
33	chr11:47295800-47319800	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr11:47295800-47320000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr11:47295800-47322000	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr11:47295800-47322400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr11:47295800-47340600	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr11:47295800-47352800	Strong transcription	Duodenum Mucosa	Duodenum
39	chr11:47296000-47317200	Strong transcription	Pancreas	Pancrea
40	chr11:47296000-47317600	Strong transcription	Gastric	stomach
41	chr11:47296000-47318800	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr11:47296000-47318800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr11:47296000-47319400	Strong transcription	Lung	lung
44	chr11:47296000-47319800	Strong transcription	Brain Anterior Caudate	brain
45	chr11:47296000-47320200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:47296000-47320400	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr11:47296000-47321400	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr11:47296000-47321800	Strong transcription	Colonic Mucosa	Colon
49	chr11:47296000-47321800	Strong transcription	Ovary	ovary
50	chr11:47296000-47322200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links