Variant report

Variant	rs2284392
Chromosome Location	chr12:21631934-21631935
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:21631339..21633803-chr12:21653800..21655829,2	K562	blood:
2	chr12:21628982..21633807-chr12:21637504..21641052,4	K562	blood:
3	chr12:21627258..21630127-chr12:21631085..21633141,2	K562	blood:

Variant related genes	Relation type
ENSG00000004700	Chromatin interaction
ENSG00000111711	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10161130	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs10161132	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10743416	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10770810	0.82[CHB][hapmap]
rs10841810	0.81[CHB][hapmap]
rs10841815	0.86[CHB][hapmap]
rs10841832	0.82[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap]
rs10841834	0.82[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs10841841	0.83[CHD][hapmap]
rs11046050	0.82[CHB][hapmap]
rs11046055	0.86[CHB][hapmap]
rs11046064	0.86[CHB][hapmap]
rs11046065	0.90[CHB][hapmap]
rs11608682	0.82[CHB][hapmap]
rs11610942	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs11612017	0.91[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs12318289	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs12372774	0.86[CHB][hapmap]
rs13035	0.82[CHB][hapmap]
rs1366	0.81[CHD][hapmap]
rs1476904	0.86[CHB][hapmap]
rs1476905	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs1476907	0.86[CHB][hapmap]
rs1860949	0.82[CHB][hapmap]
rs1963817	0.82[CHB][hapmap]
rs2058463	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs2058464	0.86[CHB][hapmap]
rs2110165	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs2159943	0.82[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap]
rs2159948	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs2192183	0.81[CHB][hapmap]
rs2215734	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs2302500	0.82[CHB][hapmap]
rs2417979	0.86[CHB][hapmap]
rs2417980	0.81[CHB][hapmap]
rs2417981	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2417982	0.81[CHB][hapmap]
rs2417984	0.86[CHB][hapmap]
rs3213212	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs3752648	0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs3759229	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs3782660	0.81[CHB][hapmap]
rs3825287	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs4762829	0.86[CHB][hapmap]
rs4762830	0.86[CHB][hapmap]
rs4762831	0.86[CHB][hapmap]
rs6487222	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs6487223	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs6487229	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs6487230	0.82[CHB][hapmap]
rs6487233	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs7134243	0.86[CHB][hapmap]
rs7135390	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs7136175	0.82[CHB][hapmap]
rs7136257	0.82[CHB][hapmap]
rs7136265	0.82[CHB][hapmap]
rs7137034	0.82[CHB][hapmap]
rs714356	0.82[CHB][hapmap]
rs714357	0.82[CHB][hapmap]
rs7295570	0.82[CHB][hapmap]
rs7303408	0.86[CHB][hapmap]
rs7310953	0.86[CHB][hapmap]
rs738028	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs7970416	0.86[CHB][hapmap]
rs917855	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs997820	0.86[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2284392	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs2284392	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs2284392	PYROXD1	cis	Esophagus Muscularis	GTEx
rs2284392	PYROXD1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21595800-21632600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:21595800-21633200	Weak transcription	Gastric	stomach
3	chr12:21595800-21650000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:21597400-21636000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:21607000-21645800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:21611000-21652800	Weak transcription	Small Intestine	intestine
7	chr12:21611000-21653600	Weak transcription	Esophagus	oesophagus
8	chr12:21611200-21640800	Weak transcription	Fetal Heart	heart
9	chr12:21614800-21652800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:21617000-21653000	Weak transcription	Colonic Mucosa	Colon
11	chr12:21619800-21638400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:21619800-21652200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr12:21619800-21652400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:21619800-21652400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr12:21620200-21652600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:21620400-21637800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:21620600-21636600	Strong transcription	Dnd41	blood
18	chr12:21620600-21652200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr12:21620800-21636600	Strong transcription	Fetal Thymus	thymus
20	chr12:21623000-21635400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:21623200-21649400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:21623400-21633400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:21623800-21636600	Strong transcription	Liver	Liver
24	chr12:21623800-21636800	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr12:21623800-21637000	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr12:21623800-21638000	Strong transcription	Placenta	Placenta
27	chr12:21623800-21639000	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr12:21623800-21639600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:21624000-21633200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:21624000-21636600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:21624000-21636600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr12:21624000-21636600	Strong transcription	GM12878-XiMat	blood
33	chr12:21624000-21636800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:21624000-21636800	Strong transcription	NHDF-Ad	bronchial
35	chr12:21624000-21637600	Strong transcription	Adipose Nuclei	Adipose
36	chr12:21624000-21638200	Strong transcription	Primary B cells from cord blood	blood
37	chr12:21624200-21637000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:21624200-21639800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:21624400-21636400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr12:21624400-21636600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr12:21624400-21636800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:21624400-21636800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:21624400-21637000	Strong transcription	HSMM	muscle
44	chr12:21624400-21638000	Strong transcription	Primary T cells from cord blood	blood
45	chr12:21624400-21638000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:21625000-21636400	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:21625000-21637400	Strong transcription	A549	lung
48	chr12:21626000-21633200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr12:21626200-21636600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:21626600-21633200	Weak transcription	H9 Cell Line	embryonic stem cell

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