Variant report

Variant	rs3850657
Chromosome Location	chr5:90337465-90337466
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10514343	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11952993	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11955946	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12188068	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12188249	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12189005	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17572843	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55792004	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56106025	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56258383	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62376462	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62376463	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62376490	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62376491	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6861614	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6880626	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6888979	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6889138	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73771166	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv882369	chr5:90275825-90344149	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 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	chr5:90324600-90350400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:90330800-90338000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:90334400-90338800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:90334600-90338800	Weak transcription	Adipose Nuclei	Adipose
5	chr5:90335000-90340600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:90335000-90340800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr5:90335000-90344000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:90335200-90344000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:90335400-90338600	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:90335400-90338600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr5:90335400-90340600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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