Variant report

Variant	rs929479
Chromosome Location	chr17:66659108-66659109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11077693	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11077698	0.97[EUR][1000 genomes]
rs11077699	0.97[EUR][1000 genomes]
rs11657717	0.97[EUR][1000 genomes]
rs11657722	0.97[EUR][1000 genomes]
rs11658862	0.97[EUR][1000 genomes]
rs12150366	0.94[EUR][1000 genomes]
rs17673884	0.97[EUR][1000 genomes]
rs4968913	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4968914	0.82[AMR][1000 genomes];0.96[EUR][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	nsv833524	chr17:66524030-66705194	Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv521432	chr17:66652594-66660827	Active TSS Enhancers Weak transcription Flanking Active TSS	lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs929479	WIPI1	cis	cerebellum	SCAN
rs929479	TEX2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66656000-66659200	Enhancers	Pancreatic Islets	Pancreatic Islet
2	chr17:66656000-66661600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr17:66656200-66659200	Enhancers	Liver	Liver
4	chr17:66657000-66659200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr17:66657200-66659400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr17:66657200-66659400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr17:66657200-66659600	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr17:66657400-66659200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr17:66658000-66659800	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr17:66658200-66659600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr17:66658200-66661200	Weak transcription	Fetal Brain Male	brain
12	chr17:66658400-66659200	Enhancers	H9 Cell Line	embryonic stem cell
13	chr17:66658800-66659400	Enhancers	H1 Cell Line	embryonic stem cell

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Input of quick search could be:

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

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