Variant report

Variant	rs1322460
Chromosome Location	chr9:8028400-8028401
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10120639	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10758922	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10815741	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10815742	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10976733	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10976734	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10976757	0.88[EUR][1000 genomes]
rs1407461	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1570326	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1575322	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146083	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2224600	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4742432	0.93[EUR][1000 genomes]
rs6477256	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7024333	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7025594	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7039072	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851010	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7861629	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9407396	0.83[EUR][1000 genomes]
rs972824	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs995315	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv995116	chr9:7682729-8065192	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv8414	chr9:7827373-8511613	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1024456	chr9:7887727-8157591	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv539979	chr9:7887727-8157591	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1032967	chr9:7985651-8088281	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv519428	chr9:7997936-8039781	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv892219	chr9:7997936-8087483	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv613279	chr9:8009428-8097977	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1028133	chr9:8015209-8116186	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv2762786	chr9:8020572-8046450	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1029422	chr9:8021065-8046438	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1322460	PPP1R16A	trans	brain	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8025200-8032600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr9:8026400-8028800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:8027200-8028400	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr9:8027400-8028400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr9:8028000-8028400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:8028200-8033800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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