Variant report

Variant	rs12889262
Chromosome Location	chr14:20784117-20784118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1000608	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1057605	0.87[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs1132644	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11623831	0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs11845291	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11848535	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12588213	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12890140	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1713418	0.83[MEX][hapmap]
rs1713419	0.83[MEX][hapmap]
rs1889361	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1889363	0.81[ASW][hapmap];0.89[LWK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs1953549	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1953552	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2001572	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28436942	0.81[AFR][1000 genomes]
rs28500547	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3784244	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4451865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981975	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6575132	0.85[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6575164	0.85[CEU][hapmap];0.84[CHD][hapmap];0.92[MEX][hapmap];0.81[AMR][1000 genomes]
rs6575168	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs7159947	0.88[LWK][hapmap]
rs7160770	0.85[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043923	chr14:20338742-21336425	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
2	nsv541970	chr14:20338742-21336425	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
3	nsv1037160	chr14:20517485-20901811	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
4	nsv541974	chr14:20517485-20901811	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
5	esv1806993	chr14:20743269-20841162	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
6	nsv534131	chr14:20757405-20886235	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers 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	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12889262	PARP2	cis	cerebellum	SCAN
rs12889262	PARP2	cis	parietal	SCAN
rs12889262	CCNB1IP1	cis	parietal	SCAN
rs12889262	PRMT5	cis	parietal	SCAN
rs12889262	CCNB1IP1	cis	cerebellum	SCAN
rs12889262	RPPH1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:20774200-20784400	Weak transcription	Aorta	Aorta
2	chr14:20774200-20785000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr14:20774200-20785000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:20774200-20785400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr14:20774200-20785400	Weak transcription	Thymus	Thymus
6	chr14:20774200-20785400	Weak transcription	Spleen	Spleen
7	chr14:20774200-20785600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr14:20774200-20785800	Weak transcription	Gastric	stomach
9	chr14:20774200-20786000	Weak transcription	Pancreas	Pancrea
10	chr14:20774200-20795400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr14:20774200-20795600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr14:20774200-20795600	Weak transcription	Fetal Heart	heart
13	chr14:20774200-20800400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr14:20774200-20800400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr14:20774200-20800400	Weak transcription	Fetal Brain Male	brain
16	chr14:20774200-20800400	Weak transcription	Stomach Mucosa	stomach
17	chr14:20774200-20800600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr14:20774200-20800800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr14:20774200-20800800	Weak transcription	Small Intestine	intestine
20	chr14:20774400-20784400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr14:20774400-20787200	Weak transcription	Brain Germinal Matrix	brain
22	chr14:20778800-20798600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr14:20779000-20795600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr14:20779400-20787000	Strong transcription	Fetal Muscle Trunk	muscle
25	chr14:20779400-20788400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr14:20779400-20788600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr14:20779400-20788800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr14:20779400-20788800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr14:20779400-20790200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr14:20779400-20794000	Strong transcription	Left Ventricle	heart
31	chr14:20779400-20794200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr14:20779400-20794800	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr14:20779400-20794800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr14:20779400-20795000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr14:20779400-20795000	Strong transcription	Osteobl	bone
36	chr14:20779400-20795200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr14:20779400-20795200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr14:20779400-20795400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr14:20779400-20797000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr14:20779400-20797200	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr14:20779400-20797800	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr14:20779400-20798000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr14:20779400-20799000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr14:20779600-20784400	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr14:20779600-20784800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr14:20779600-20784800	Strong transcription	Fetal Thymus	thymus
47	chr14:20779600-20784800	Strong transcription	HMEC	breast
48	chr14:20779600-20784800	Strong transcription	K562	blood
49	chr14:20779600-20784800	Strong transcription	NHDF-Ad	bronchial
50	chr14:20779600-20785000	Strong transcription	GM12878-XiMat	blood

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