Variant report

Variant	rs3910952
Chromosome Location	chr19:38292369-38292370
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10401281	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10402530	0.81[ASN][1000 genomes]
rs10404567	0.91[CHB][hapmap];0.95[CHD][hapmap];0.80[JPT][hapmap]
rs10420595	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10420891	0.81[ASN][1000 genomes]
rs11878269	0.82[ASN][1000 genomes]
rs11879180	0.81[ASN][1000 genomes]
rs12975057	0.81[ASN][1000 genomes]
rs1643466	0.90[CHB][hapmap]
rs1643467	0.90[CHB][hapmap]
rs1643468	0.90[CHB][hapmap]
rs2068431	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2075281	0.95[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs2075283	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2305105	0.85[EUR][1000 genomes]
rs2382623	0.89[CEU][hapmap]
rs353414	0.91[CHB][hapmap]
rs353423	0.91[CHB][hapmap]
rs3848625	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3848626	0.85[ASN][1000 genomes]
rs4802135	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs4803524	0.95[CHB][hapmap];0.98[CHD][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs4803525	0.85[EUR][1000 genomes]
rs4803528	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58449039	0.81[ASN][1000 genomes]
rs705492	0.95[CHB][hapmap]
rs705494	0.95[CHB][hapmap];0.95[CHD][hapmap]
rs705496	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs7245864	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7250409	0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[JPT][hapmap]
rs8101752	0.85[ASN][1000 genomes]
rs8102579	0.95[CHB][hapmap];0.98[CHD][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs8104076	0.82[ASN][1000 genomes]
rs8108245	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs8110284	0.95[CHB][hapmap]
rs8182498	0.81[ASN][1000 genomes]
rs833895	0.95[CHB][hapmap]
rs833914	0.91[CHB][hapmap]

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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv960835	chr19:38270238-38293706	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1057428	chr19:38282158-38320814	Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3910952	PSMC4	cis	parietal	SCAN
rs3910952	ZNF585B	cis	Artery Tibial	GTEx
rs3910952	TRAPPC6A	cis	cerebellum	SCAN
rs3910952	ARHGEF1	cis	cerebellum	SCAN
rs3910952	TMEM145	cis	parietal	SCAN
rs3910952	AC012309.5	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38291600-38296000	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr19:38291800-38295400	ZNF genes & repeats	Brain Hippocampus Middle	brain
3	chr19:38291800-38295400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum

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