Variant report

Variant	rs2416458
Chromosome Location	chr5:116293114-116293115
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10035261	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10037847	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10039238	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10040194	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10040196	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10071164	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10074601	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10075567	0.85[EUR][1000 genomes]
rs10076519	0.81[EUR][1000 genomes]
rs10079735	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10478319	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10478320	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11241409	0.86[EUR][1000 genomes]
rs12719224	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13157896	0.89[ASN][1000 genomes]
rs13175694	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13181718	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1459083	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1459085	0.85[EUR][1000 genomes]
rs1459091	0.88[ASN][1000 genomes]
rs1459092	0.84[EUR][1000 genomes]
rs1459094	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1459095	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1903111	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2168996	0.85[EUR][1000 genomes]
rs2199145	0.85[EUR][1000 genomes]
rs4512160	0.85[EUR][1000 genomes]
rs4583923	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4920944	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6594991	0.84[EUR][1000 genomes]
rs6594993	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6594994	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6594995	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6594996	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6595001	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6862230	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6866207	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6868388	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6886797	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6897596	0.83[EUR][1000 genomes]
rs7701572	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7706678	0.86[EUR][1000 genomes]
rs7716867	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7730991	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9285886	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9327023	0.83[EUR][1000 genomes]
rs979883	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][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	nsv527974	chr5:115987168-116303678	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1033140	chr5:116035131-116314673	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1020292	chr5:116183712-116349633	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1033379	chr5:116244963-116464338	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1017455	chr5:116261466-116302129	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv969206	chr5:116288516-116300472	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:116289800-116295000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr5:116289800-116297000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:116290000-116293200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr5:116290600-116299600	Weak transcription	Brain Substantia Nigra	brain
5	chr5:116291000-116293400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:116293000-116293600	Enhancers	Brain Hippocampus Middle	brain

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