Variant report

Variant	rs11046078
Chromosome Location	chr12:21634891-21634892
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:21632020..21637029-chr12:21648453..21652691,4	K562	blood:
2	chr12:21633395..21635663-chr12:21646507..21648345,2	MCF-7	breast:
3	chr12:21629462..21631734-chr12:21633503..21635261,2	K562	blood:
4	chr12:21632280..21634944-chr12:21765213..21766977,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10743416	0.85[ASN][1000 genomes]
rs10841834	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11612017	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12318289	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2159943	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2215730	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3213212	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487233	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][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	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1054220	chr12:21612158-21692103	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1036084	chr12:21631009-21792756	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11046078	RECQL	Cis_1M	lymphoblastoid	RTeQTL
rs11046078	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs11046078	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs11046078	LOC642732	Cis_1M	lymphoblastoid	RTeQTL
rs11046078	PYROXD1	cis	Esophagus Muscularis	GTEx
rs11046078	PYROXD1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21595800-21650000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:21597400-21636000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:21607000-21645800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:21611000-21652800	Weak transcription	Small Intestine	intestine
5	chr12:21611000-21653600	Weak transcription	Esophagus	oesophagus
6	chr12:21611200-21640800	Weak transcription	Fetal Heart	heart
7	chr12:21614800-21652800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:21617000-21653000	Weak transcription	Colonic Mucosa	Colon
9	chr12:21619800-21638400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:21619800-21652200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr12:21619800-21652400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:21619800-21652400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr12:21620200-21652600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:21620400-21637800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:21620600-21636600	Strong transcription	Dnd41	blood
16	chr12:21620600-21652200	Strong transcription	Primary B cells from peripheral blood	blood
17	chr12:21620800-21636600	Strong transcription	Fetal Thymus	thymus
18	chr12:21623000-21635400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:21623200-21649400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:21623800-21636600	Strong transcription	Liver	Liver
21	chr12:21623800-21636800	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr12:21623800-21637000	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr12:21623800-21638000	Strong transcription	Placenta	Placenta
24	chr12:21623800-21639000	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr12:21623800-21639600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:21624000-21636600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr12:21624000-21636600	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr12:21624000-21636600	Strong transcription	GM12878-XiMat	blood
29	chr12:21624000-21636800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:21624000-21636800	Strong transcription	NHDF-Ad	bronchial
31	chr12:21624000-21637600	Strong transcription	Adipose Nuclei	Adipose
32	chr12:21624000-21638200	Strong transcription	Primary B cells from cord blood	blood
33	chr12:21624200-21637000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:21624200-21639800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:21624400-21636400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr12:21624400-21636600	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:21624400-21636800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:21624400-21636800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:21624400-21637000	Strong transcription	HSMM	muscle
40	chr12:21624400-21638000	Strong transcription	Primary T cells from cord blood	blood
41	chr12:21624400-21638000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr12:21625000-21636400	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:21625000-21637400	Strong transcription	A549	lung
44	chr12:21626200-21636600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr12:21626600-21641000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:21627000-21635800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr12:21628000-21635000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr12:21628000-21636000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr12:21628200-21649200	Weak transcription	HepG2	liver
50	chr12:21628800-21636400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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