Variant report

Variant	rs7645341
Chromosome Location	chr3:140500654-140500655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11707358	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11711297	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11712438	0.87[EUR][1000 genomes]
rs11712759	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11714350	0.84[AMR][1000 genomes]
rs11716917	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11716928	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11717493	0.87[EUR][1000 genomes]
rs11719496	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497874	0.87[EUR][1000 genomes]
rs2090612	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2090613	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2102875	0.82[AMR][1000 genomes]
rs2102876	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28464411	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28720697	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28821624	0.87[EUR][1000 genomes]
rs4331654	0.87[EUR][1000 genomes]
rs4422276	0.87[EUR][1000 genomes]
rs4428155	0.87[EUR][1000 genomes]
rs4465920	0.89[EUR][1000 genomes]
rs56016520	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56250118	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56337530	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs58714532	0.87[EUR][1000 genomes]
rs62266035	0.84[AMR][1000 genomes]
rs62266471	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769067	0.85[EUR][1000 genomes]
rs72987149	0.87[EUR][1000 genomes]
rs73233060	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7627345	0.86[EUR][1000 genomes]
rs7630311	0.82[ASN][1000 genomes]
rs7632490	0.87[EUR][1000 genomes]
rs7632807	0.87[EUR][1000 genomes]
rs7634405	0.88[EUR][1000 genomes]
rs7639879	0.87[EUR][1000 genomes]
rs7644487	0.87[EUR][1000 genomes]
rs7645310	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649697	0.88[EUR][1000 genomes]
rs9811819	0.88[EUR][1000 genomes]
rs9825227	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835982	0.82[AMR][1000 genomes]
rs9845912	0.87[EUR][1000 genomes]
rs9861350	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1008838	chr3:140355975-140588726	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv877547	chr3:140366948-140575287	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv829743	chr3:140384246-140559778	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv591865	chr3:140396022-140728850	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv1005522	chr3:140454632-140685915	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv536732	chr3:140454632-140685915	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7645341	CLSTN2	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140499800-140502200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:140500000-140500800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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