Variant report

Variant	rs16962955
Chromosome Location	chr15:50140016-50140017
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50137595..50140472-chr15:50174008..50176378,2	K562	blood:
2	chr15:50138908..50140923-chr15:50168634..50171590,2	MCF-7	breast:
3	chr15:50138152..50141031-chr15:50143945..50145459,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104043	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11070732	0.93[ASN][1000 genomes]
rs11635372	0.88[ASN][1000 genomes]
rs11855174	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12909220	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12909948	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs16962929	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16962997	0.87[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16963008	0.87[CEU][hapmap]
rs16963010	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs1911609	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs28369666	0.88[ASN][1000 genomes]
rs28391660	0.83[ASN][1000 genomes]
rs34693309	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34760149	0.91[ASN][1000 genomes]
rs4414432	0.93[CEU][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs57169939	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60020506	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61347161	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493382	0.89[ASN][1000 genomes]
rs7178500	0.92[ASN][1000 genomes]
rs7180532	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7181711	0.91[ASN][1000 genomes]
rs8028196	0.85[ASN][1000 genomes]
rs8030539	0.88[ASN][1000 genomes]
rs8034348	0.91[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.96[ASN][1000 genomes]
rs8042949	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv833003	chr15:50100372-50273309	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16962955	MEIS2	trans	brain	seeQTL
rs16962955	USP50	cis	cerebellum	SCAN
rs16962955	SPATA5L1	cis	cerebellum	SCAN
rs16962955	CASC4	cis	parietal	SCAN
rs16962955	GALK2	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50132400-50141200	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr15:50134400-50140200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:50134800-50140200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr15:50135200-50181400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr15:50135800-50187400	Weak transcription	Liver	Liver
6	chr15:50136600-50149000	Weak transcription	Placenta	Placenta
7	chr15:50137800-50141600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr15:50138000-50146800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr15:50138200-50142600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:50138200-50145200	Strong transcription	Primary hematopoietic stem cells	blood
11	chr15:50138200-50189800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr15:50138400-50140800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:50138800-50140800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr15:50138800-50142200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:50138800-50142400	Enhancers	Hela-S3	cervix
16	chr15:50139000-50141400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr15:50139000-50142400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:50139200-50142000	Enhancers	NHLF	lung
19	chr15:50139200-50142200	Enhancers	NH-A	brain
20	chr15:50139400-50140200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:50139600-50140200	Enhancers	Ovary	ovary
22	chr15:50139600-50140200	Flanking Active TSS	Osteobl	bone
23	chr15:50139600-50140400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr15:50139600-50141000	Enhancers	Adipose Nuclei	Adipose
25	chr15:50139600-50141000	Enhancers	Fetal Stomach	stomach
26	chr15:50139600-50141000	Enhancers	Stomach Mucosa	stomach
27	chr15:50139600-50141200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:50139600-50141200	Enhancers	HSMMtube	muscle
29	chr15:50139600-50141400	Enhancers	Colon Smooth Muscle	Colon
30	chr15:50139600-50141400	Enhancers	HSMM	muscle
31	chr15:50139800-50140200	Flanking Active TSS	A549	lung
32	chr15:50139800-50140400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:50139800-50140400	Flanking Active TSS	NHDF-Ad	bronchial
34	chr15:50139800-50140800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:50139800-50141000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:50140000-50141200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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