Variant report

Variant	rs28639589
Chromosome Location	chr6:117710661-117710662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10434878	0.93[LWK][hapmap];0.85[YRI][hapmap]
rs11153658	1.00[ASW][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4946255	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs9320599	0.83[LWK][hapmap]
rs9374656	0.89[AFR][1000 genomes]
rs9387470	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9387471	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9387476	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs9401002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28639589	SATB1	trans	lymphoblastoid	seeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117662000-117717200	Weak transcription	HSMMtube	muscle
2	chr6:117692600-117735800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:117692800-117717400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:117707400-117715800	Weak transcription	HSMM	muscle
5	chr6:117708000-117714200	Enhancers	Liver	Liver
6	chr6:117708800-117713000	Enhancers	Fetal Intestine Large	intestine
7	chr6:117709000-117712200	Enhancers	HepG2	liver
8	chr6:117709200-117711600	Enhancers	Fetal Intestine Small	intestine
9	chr6:117709600-117713800	Weak transcription	Stomach Mucosa	stomach
10	chr6:117710000-117711600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:117710400-117711600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:117710600-117711000	Enhancers	A549	lung
13	chr6:117710600-117711000	Flanking Active TSS	HMEC	breast
14	chr6:117710600-117711400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:117710600-117711600	Enhancers	NHEK	skin

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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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