Variant report

Variant	rs16962929
Chromosome Location	chr15:50103026-50103027
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:50090867..50093213-chr15:50102462..50104397,2	K562	blood:
2	chr15:50101806..50104896-chr15:50108542..50111577,3	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11070732	0.80[ASN][1000 genomes]
rs11855174	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12902281	0.81[JPT][hapmap]
rs12909220	0.95[JPT][hapmap]
rs12909948	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs16962955	0.93[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16962997	0.95[JPT][hapmap]
rs16963008	0.80[CEU][hapmap]
rs16963010	0.80[CEU][hapmap];0.80[JPT][hapmap]
rs1911609	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28369666	0.82[ASN][1000 genomes]
rs34693309	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4414432	0.86[CEU][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs57169939	0.91[EUR][1000 genomes]
rs60020506	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61347161	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493382	0.82[ASN][1000 genomes]
rs7178500	0.81[ASN][1000 genomes]
rs7180532	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8034348	0.80[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1528	chr15:50067958-50112958	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1047047	chr15:50070224-50125096	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1042311	chr15:50083175-50125096	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2761888	chr15:50083187-50125108	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv542381	chr15:50086150-50115876	Enhancers Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16962929	USP50	cis	cerebellum	SCAN
rs16962929	SPATA5L1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50100400-50103200	Enhancers	Hela-S3	cervix
2	chr15:50101200-50103200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr15:50101800-50103200	Enhancers	Fetal Muscle Leg	muscle
4	chr15:50102200-50107400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:50102400-50103200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:50102400-50107800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:50102600-50103200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr15:50102600-50103200	Enhancers	Adipose Nuclei	Adipose
9	chr15:50102800-50103200	Enhancers	Colon Smooth Muscle	Colon
10	chr15:50102800-50103200	Enhancers	Rectal Smooth Muscle	rectum
11	chr15:50102800-50103400	Weak transcription	Fetal Lung	lung
12	chr15:50103000-50105800	Weak transcription	Fetal Stomach	stomach
13	chr15:50103000-50106000	Weak transcription	Ovary	ovary
14	chr15:50103000-50107800	Weak transcription	Aorta	Aorta

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