Variant report

Variant	rs12533454
Chromosome Location	chr7:152887205-152887206
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:152876321..152879731-chr7:152886196..152889349,3	K562	blood:
2	chr7:152886505..152888240-chr7:153106300..153108850,2	K562	blood:
3	chr7:152886507..152888458-chr7:153102294..153104030,2	K562	blood:
4	chr7:152886558..152889278-chr7:152891243..152892822,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10225319	0.81[EUR][1000 genomes]
rs10232853	0.83[EUR][1000 genomes]
rs10242161	0.81[EUR][1000 genomes]
rs10242169	0.81[EUR][1000 genomes]
rs10246727	0.81[EUR][1000 genomes]
rs10248771	0.81[EUR][1000 genomes]
rs10257436	0.81[EUR][1000 genomes]
rs10276503	0.81[EUR][1000 genomes]
rs10276585	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10280270	0.80[EUR][1000 genomes]
rs10808002	0.81[EUR][1000 genomes]
rs10952394	0.80[EUR][1000 genomes]
rs11533977	0.85[EUR][1000 genomes]
rs11767856	0.81[EUR][1000 genomes]
rs12333395	0.81[EUR][1000 genomes]
rs12531525	0.85[EUR][1000 genomes]
rs12533582	0.96[EUR][1000 genomes]
rs12538130	0.80[EUR][1000 genomes]
rs12667772	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13308368	0.80[EUR][1000 genomes]
rs13308608	0.80[EUR][1000 genomes]
rs2312598	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2312600	0.96[EUR][1000 genomes]
rs28534796	0.80[EUR][1000 genomes]
rs34584710	0.80[EUR][1000 genomes]
rs4236445	0.85[EUR][1000 genomes]
rs4236446	0.81[EUR][1000 genomes]
rs4357210	0.80[EUR][1000 genomes]
rs4364561	0.80[EUR][1000 genomes]
rs4380843	0.81[EUR][1000 genomes]
rs4407788	0.80[EUR][1000 genomes]
rs4500004	0.80[EUR][1000 genomes]
rs4613898	0.80[EUR][1000 genomes]
rs4644150	0.81[EUR][1000 genomes]
rs4999662	0.88[EUR][1000 genomes]
rs56014150	0.81[EUR][1000 genomes]
rs58323924	0.81[EUR][1000 genomes]
rs60917153	0.81[EUR][1000 genomes]
rs61359548	0.81[EUR][1000 genomes]
rs6951978	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970695	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7788751	0.81[EUR][1000 genomes]
rs7788918	0.81[EUR][1000 genomes]
rs7800608	0.80[EUR][1000 genomes]
rs7801115	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027100	chr7:152294734-152935140	Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv868873	chr7:152371297-152900113	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv532222	chr7:152504090-153450290	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv831194	chr7:152762400-152963937	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv889509	chr7:152868624-153005933	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12533454	GALNTL5	cis	cerebellum	SCAN
rs12533454	CDK5	cis	parietal	SCAN
rs12533454	ZNF467	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:152873600-152890400	Weak transcription	Right Atrium	heart
2	chr7:152886600-152888400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:152886800-152887400	Enhancers	Placenta	Placenta

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