Variant report

Variant	rs9688553
Chromosome Location	chr6:117991120-117991121
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12111126	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28522156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28628829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9689787	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv5449	chr6:117954646-117999751	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr6:117969400-117995800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr6:117973800-117995600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:117978000-117995600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:117985800-117991200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:117990000-117991400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr6:117990000-117992200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
7	chr6:117990400-117995000	Weak transcription	HepG2	liver
8	chr6:117990600-117991800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
9	chr6:117990600-117995200	Weak transcription	Brain Hippocampus Middle	brain
10	chr6:117990600-117995800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr6:117991000-117991800	ZNF genes & repeats	ES-UCSF4 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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