Variant report

Variant	rs13100388
Chromosome Location	chr3:89383148-89383149
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11128072	0.82[EUR][1000 genomes]
rs11923303	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13076853	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13088663	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1398532	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1398535	0.83[EUR][1000 genomes]
rs1512907	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1512912	0.81[EUR][1000 genomes]
rs1567732	0.82[EUR][1000 genomes]
rs17800641	0.82[EUR][1000 genomes]
rs28675360	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28885734	0.80[EUR][1000 genomes]
rs35173319	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35448293	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35511518	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4449340	0.83[EUR][1000 genomes]
rs4857496	0.81[EUR][1000 genomes]
rs6551409	0.81[EUR][1000 genomes]
rs6768381	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6770978	0.80[EUR][1000 genomes]
rs6771336	0.81[EUR][1000 genomes]
rs7619025	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs907712	0.83[EUR][1000 genomes]
rs9310119	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9310120	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9310121	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9310122	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs954964	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9809011	0.85[EUR][1000 genomes]
rs9811041	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9817553	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9833400	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9846844	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9853389	0.81[EUR][1000 genomes]
rs9866945	0.85[EUR][1000 genomes]
rs9866959	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9877953	0.81[EUR][1000 genomes]
rs994129	0.82[EUR][1000 genomes]
rs9990016	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv437866	chr3:89247881-89480265	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv590921	chr3:89294149-89392778	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv590922	chr3:89314862-89417064	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv590923	chr3:89336417-89417171	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1001345	chr3:89368629-89444995	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1000694	chr3:89373820-89453045	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv590924	chr3:89375433-89417287	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv590925	chr3:89379935-89417171	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv590926	chr3:89379935-89417287	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv590927	chr3:89379935-89418262	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1013893	chr3:89381141-89419369	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1008018	chr3:89382031-90254063	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv536639	chr3:89382031-90254063	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89379400-89384000	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr3:89382000-89383600	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr3:89382200-89383200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:89382400-89383400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:89382400-89383800	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr3:89382400-89391200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:89382800-89383200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:89382800-89391000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:89383000-89383800	Weak transcription	Fetal Brain Female	brain
10	chr3:89383000-89384000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr3:89383000-89390200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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