Variant report

Variant	rs1390911
Chromosome Location	chr4:44932251-44932252
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10016495	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10938374	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1111981	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11723242	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11938368	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12505745	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12509720	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13105769	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13127633	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs13133064	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13139707	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1390924	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1390927	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1496981	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1496994	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1587239	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1845949	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1908807	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28526098	1.00[ASN][1000 genomes]
rs2882025	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4074007	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4694791	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4695065	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4695066	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6447390	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6447391	0.97[ASN][1000 genomes]
rs6847133	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6850886	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7656009	0.96[ASN][1000 genomes]
rs7657226	0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7675888	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7680743	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7684987	0.86[AMR][1000 genomes]
rs9291254	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9759704	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531944	chr4:44299343-45200700	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1013488	chr4:44543808-44976123	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv915992	chr4:44705614-44972966	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1014327	chr4:44735209-45218149	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv878979	chr4:44871931-45102488	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv432591	chr4:44922068-45017576	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1390911	GNPDA2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:44929400-44932400	Enhancers	Fetal Heart	heart
2	chr4:44930000-44959400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:44932000-44932400	Enhancers	Fetal Brain Male	brain

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