Variant report

Variant	rs12902190
Chromosome Location	chr15:59692974-59692975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11071434	0.92[JPT][hapmap]
rs11071435	0.83[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.81[ASN][1000 genomes]
rs11071438	0.82[ASN][1000 genomes]
rs11854940	0.83[ASN][1000 genomes]
rs12372986	0.82[ASN][1000 genomes]
rs12593938	0.84[JPT][hapmap]
rs12908836	0.83[ASN][1000 genomes]
rs12910391	0.83[ASN][1000 genomes]
rs12913287	0.82[ASN][1000 genomes]
rs1484282	0.83[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs4774329	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs71480523	0.83[ASN][1000 genomes]
rs900828	0.83[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.83[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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv934082	chr15:59608605-59733211	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv904275	chr15:59648633-59726610	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	n/a
4	nsv904276	chr15:59648633-59743010	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	n/a
5	nsv904277	chr15:59666992-59705005	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
6	nsv524569	chr15:59666992-59712427	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12902190	WDR72	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59675200-59703000	Weak transcription	Aorta	Aorta
2	chr15:59678000-59693400	Weak transcription	Liver	Liver
3	chr15:59681400-59694200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:59688400-59698800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr15:59689200-59693800	Weak transcription	A549	lung
6	chr15:59690400-59694200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr15:59690600-59693000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:59690800-59695600	Weak transcription	Lung	lung
9	chr15:59690800-59702600	Weak transcription	Left Ventricle	heart
10	chr15:59691200-59693000	Enhancers	Adipose Nuclei	Adipose
11	chr15:59691400-59693000	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr15:59691400-59693200	Flanking Active TSS	GM12878-XiMat	blood
13	chr15:59691400-59693600	Enhancers	Brain Substantia Nigra	brain
14	chr15:59691400-59693800	Enhancers	Brain Hippocampus Middle	brain
15	chr15:59691600-59693000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr15:59691800-59693000	Enhancers	Spleen	Spleen
17	chr15:59691800-59693000	Bivalent Enhancer	HepG2	liver
18	chr15:59691800-59693000	Enhancers	HMEC	breast
19	chr15:59691800-59693600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
20	chr15:59691800-59693600	Enhancers	Placenta	Placenta
21	chr15:59691800-59694600	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr15:59692000-59693000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr15:59692000-59694800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
24	chr15:59692200-59693000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
25	chr15:59692200-59693000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:59692200-59693600	Enhancers	Brain Anterior Caudate	brain
27	chr15:59692400-59693000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
28	chr15:59692400-59693400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr15:59692400-59693800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
30	chr15:59692600-59693000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr15:59692600-59693000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:59692600-59693000	Enhancers	Fetal Thymus	thymus
33	chr15:59692600-59693000	Enhancers	Pancreas	Pancrea
34	chr15:59692600-59693200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
35	chr15:59692600-59694000	Weak transcription	Stomach Mucosa	stomach
36	chr15:59692600-59694800	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr15:59692600-59698000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr15:59692600-59701400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:59692800-59693200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
40	chr15:59692800-59693200	Enhancers	Brain Cingulate Gyrus	brain
41	chr15:59692800-59694200	Weak transcription	Small Intestine	intestine
42	chr15:59692800-59694600	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr15:59692800-59694800	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr15:59692800-59694800	Enhancers	Primary B cells from peripheral blood	blood
45	chr15:59692800-59694800	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr15:59692800-59694800	Enhancers	Brain Germinal Matrix	brain
47	chr15:59692800-59695600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr15:59692800-59698200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr15:59692800-59704800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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