Variant report

Variant	rs9860409
Chromosome Location	chr3:161144141-161144142
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs6796291	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7645213	0.85[AMR][1000 genomes]
rs9290082	0.85[AMR][1000 genomes]
rs9290083	0.85[AMR][1000 genomes]
rs9809919	0.85[AMR][1000 genomes]
rs9810022	0.85[AMR][1000 genomes]
rs9829610	0.85[AMR][1000 genomes]
rs9839583	0.85[AMR][1000 genomes]
rs9846788	0.85[AMR][1000 genomes]
rs9852701	0.85[AMR][1000 genomes]
rs9855567	1.00[AFR][1000 genomes];1.00[AMR][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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv877710	chr3:161087857-161245414	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161134400-161145200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:161134400-161148200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:161140200-161145400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:161141200-161144800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:161141400-161144200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:161141400-161144200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:161141400-161144400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:161141400-161144800	Weak transcription	HepG2	liver
9	chr3:161141400-161145200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:161141600-161144200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:161141600-161144200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:161141800-161144200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:161143800-161145200	Enhancers	HUES48 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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