Variant report

Variant	rs6440372
Chromosome Location	chr3:145508193-145508194
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs12695799	0.98[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4681256	0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4681257	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681258	0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4681259	0.94[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4681260	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681261	0.84[ASN][1000 genomes]
rs4681262	0.96[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4681263	0.96[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4681264	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6414367	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440371	0.83[AFR][1000 genomes]
rs6440373	0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6440374	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440375	0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6440376	0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6440377	0.85[ASN][1000 genomes]
rs6440378	0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6440379	0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6440380	0.93[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6440381	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6440382	0.96[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6440383	0.97[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6440384	0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6440385	0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6440386	0.96[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6440387	0.96[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6770379	0.84[AFR][1000 genomes]
rs6772938	0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6782403	0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6783103	0.84[ASN][1000 genomes]
rs6783698	0.84[AFR][1000 genomes]
rs6793409	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6794778	0.84[AFR][1000 genomes]
rs6795250	0.84[AFR][1000 genomes]
rs6796627	0.95[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7427013	0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7427041	0.96[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7428367	0.84[ASN][1000 genomes]
rs7432709	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7610711	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7611049	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7611143	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7614629	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7632711	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9812691	0.84[ASN][1000 genomes]
rs9826871	0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9835009	0.85[ASN][1000 genomes]
rs9839546	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9839893	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9840138	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9840316	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9845121	0.98[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9845157	0.96[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9861465	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9872877	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877584	chr3:144903957-145833232	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv3330499	chr3:145334189-145596853	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv3379945	chr3:145351163-145679850	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv877610	chr3:145465395-145653627	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv2751980	chr3:145473020-145758194	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1013475	chr3:145478985-145750509	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1010509	chr3:145478985-145757483	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1005624	chr3:145486437-145750509	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv999344	chr3:145506353-145750883	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv536757	chr3:145506353-145750883	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	esv33307	chr3:145506383-145667833	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6440372	WWTR1	cis	parietal	SCAN
rs6440372	UBQLN4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145507800-145508200	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr3:145507800-145508600	Weak transcription	Gastric	stomach
3	chr3:145508000-145508800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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