Variant report

Variant	rs1586892
Chromosome Location	chr4:125367740-125367741
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1388993	1.00[EUR][1000 genomes]
rs1388995	1.00[EUR][1000 genomes]
rs1492751	1.00[EUR][1000 genomes]
rs17008215	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17008226	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17008233	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17008247	1.00[EUR][1000 genomes]
rs2100621	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28701501	1.00[AFR][1000 genomes]
rs2893091	1.00[EUR][1000 genomes]
rs57627207	1.00[EUR][1000 genomes]
rs58898118	1.00[EUR][1000 genomes]
rs72923360	1.00[EUR][1000 genomes]
rs72923361	1.00[EUR][1000 genomes]
rs72923363	1.00[EUR][1000 genomes]
rs72923389	1.00[EUR][1000 genomes]
rs72923400	1.00[EUR][1000 genomes]
rs7667465	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868977	chr4:124841128-125550637	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv432624	chr4:125013395-125367740	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv998024	chr4:125019384-125380876	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv537241	chr4:125019384-125380876	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1015049	chr4:125037090-125393067	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv879880	chr4:125174817-125494547	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv2760890	chr4:125273456-125466931	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv879881	chr4:125280852-125448288	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv3339982	chr4:125357396-125380067	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1586892	STAG3	trans	lymphoblastoid	seeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:125358000-125370000	Weak transcription	Gastric	stomach
2	chr4:125359400-125370600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:125360200-125369800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:125366400-125367800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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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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