Variant report

Variant	rs12222581
Chromosome Location	chr11:47342019-47342020
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47339728..47342271-chr11:47350100..47351829,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1051006	0.81[AMR][1000 genomes]
rs10769252	0.82[AFR][1000 genomes]
rs10838685	0.84[AMR][1000 genomes]
rs10838686	0.83[AMR][1000 genomes]
rs10838687	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10838689	0.86[AMR][1000 genomes]
rs10838690	0.87[AFR][1000 genomes]
rs10838692	0.84[AFR][1000 genomes]
rs11530166	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12575456	0.83[AFR][1000 genomes]
rs1375688	0.85[AFR][1000 genomes]
rs1449626	0.81[AMR][1000 genomes]
rs2254240	0.84[AMR][1000 genomes]
rs2279238	0.81[AMR][1000 genomes]
rs2290146	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2290148	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2305280	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3729802	0.82[AMR][1000 genomes]
rs3729804	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs3729805	0.89[AMR][1000 genomes]
rs3781622	0.81[AFR][1000 genomes]
rs3847502	0.85[AFR][1000 genomes]
rs4752824	0.85[AFR][1000 genomes]
rs4752825	0.85[AFR][1000 genomes]
rs4752977	0.83[AMR][1000 genomes]
rs4752978	0.84[AMR][1000 genomes]
rs4752979	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4752983	0.87[AMR][1000 genomes]
rs59567949	0.81[AMR][1000 genomes]
rs6485751	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7120957	0.87[AFR][1000 genomes]
rs7124958	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7127907	0.85[AFR][1000 genomes]
rs753993	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7940809	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12222581	ACP2	Cis_1M	lymphoblastoid	RTeQTL
rs12222581	ACP2	cis	Thyroid	GTEx

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	chr11:47295400-47352600	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr11:47295800-47352800	Strong transcription	Duodenum Mucosa	Duodenum
4	chr11:47296000-47353600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr11:47311800-47348800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:47323400-47352400	Strong transcription	Thymus	Thymus
7	chr11:47324200-47354600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr11:47324600-47346800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:47324800-47352600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr11:47325000-47352400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr11:47325000-47352800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr11:47325200-47344000	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr11:47325200-47347000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:47325400-47346600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr11:47325400-47349200	Strong transcription	Fetal Thymus	thymus
16	chr11:47325400-47353000	Strong transcription	Fetal Intestine Small	intestine
17	chr11:47326000-47353600	Strong transcription	Fetal Stomach	stomach
18	chr11:47327800-47352200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:47328200-47351400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr11:47330800-47345200	Weak transcription	Stomach Mucosa	stomach
21	chr11:47331400-47345800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr11:47333000-47349400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:47333400-47346200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr11:47333600-47342600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr11:47333800-47345000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr11:47333800-47350600	Weak transcription	Psoas Muscle	Psoas
27	chr11:47334200-47342800	Weak transcription	Gastric	stomach
28	chr11:47335200-47343400	Weak transcription	Right Ventricle	heart
29	chr11:47336400-47350400	Weak transcription	HMEC	breast
30	chr11:47336600-47346800	Weak transcription	NHDF-Ad	bronchial
31	chr11:47337000-47342600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr11:47337000-47342800	Weak transcription	Pancreas	Pancrea
33	chr11:47337000-47343200	Weak transcription	Aorta	Aorta
34	chr11:47337000-47345000	Weak transcription	NHLF	lung
35	chr11:47337000-47345200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr11:47337000-47345400	Weak transcription	NHEK	skin
37	chr11:47337200-47343200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:47337400-47348400	Weak transcription	Small Intestine	intestine
39	chr11:47338600-47342600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr11:47338600-47343600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr11:47338800-47345000	Weak transcription	Esophagus	oesophagus
42	chr11:47338800-47347200	Weak transcription	Fetal Heart	heart
43	chr11:47338800-47356200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr11:47339000-47342800	Weak transcription	Ovary	ovary
45	chr11:47339000-47344400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr11:47339000-47345000	Weak transcription	Colon Smooth Muscle	Colon
47	chr11:47339000-47346800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr11:47339200-47342800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr11:47339200-47342800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr11:47339200-47342800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links