Variant report

Variant	rs13354091
Chromosome Location	chr5:152729750-152729751
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10036163	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10037511	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10045698	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10060758	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11738200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739127	0.97[EUR][1000 genomes]
rs11741001	0.98[EUR][1000 genomes]
rs11742907	0.98[EUR][1000 genomes]
rs11749295	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12655112	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs17114459	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17114463	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114466	0.98[EUR][1000 genomes]
rs17114473	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58361474	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs72799249	0.98[EUR][1000 genomes]
rs72799252	0.98[EUR][1000 genomes]
rs72799253	0.98[EUR][1000 genomes]
rs72799254	0.98[EUR][1000 genomes]
rs72799261	0.98[EUR][1000 genomes]
rs72799264	0.98[EUR][1000 genomes]
rs72799267	0.95[EUR][1000 genomes]
rs7703714	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7709157	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7727282	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023676	chr5:151979253-152925064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv537927	chr5:151979253-152925064	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1019051	chr5:152550863-153057896	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv868912	chr5:152582002-153095306	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1023125	chr5:152688178-152730408	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv883052	chr5:152696107-152749009	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv883053	chr5:152696107-152806220	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13354091	ZNF300P1	cis	cerebellum	SCAN
rs13354091	DCTN4	cis	cerebellum	SCAN
rs13354091	NMUR2	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:152729000-152730200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
2	chr5:152729000-152730200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr5:152729000-152730200	Enhancers	Brain Germinal Matrix	brain
4	chr5:152729000-152730600	Enhancers	H1 Cell Line	embryonic stem cell
5	chr5:152729200-152729800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:152729200-152729800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr5:152729200-152730600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr5:152729400-152729800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr5:152729400-152729800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr5:152729400-152730000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:152729400-152730000	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr5:152729400-152730200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:152729600-152729800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr5:152729600-152729800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr5:152729600-152729800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr5:152729600-152730200	Enhancers	Brain Hippocampus Middle	brain
17	chr5:152729600-152730400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:152729600-152730400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:152729600-152730800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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