Variant report

Variant	rs9485528
Chromosome Location	chr6:102114780-102114781
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10872738	0.83[LWK][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap]
rs1337415	0.86[TSI][hapmap]
rs1415483	0.81[CHB][hapmap];0.82[GIH][hapmap]
rs1415489	0.82[CEU][hapmap]
rs2065938	0.90[TSI][hapmap]
rs2105118	0.83[CEU][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2518303	0.90[TSI][hapmap]
rs2786246	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2786251	0.93[TSI][hapmap]
rs2852558	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2852559	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4839800	0.82[CEU][hapmap]
rs6904687	0.80[CEU][hapmap];0.93[YRI][hapmap]
rs7451268	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7739084	0.81[CHB][hapmap]
rs9322602	0.89[YRI][hapmap]
rs9485526	0.89[YRI][hapmap]
rs9498658	0.89[YRI][hapmap]
rs9498662	0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv538392	chr6:101938381-102148360	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv3384771	chr6:101996253-102283808	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1032499	chr6:102069885-102720998	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv463993	chr6:102084491-102165329	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv604317	chr6:102084491-102165329	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv521403	chr6:102114780-102116069	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
7	nsv527973	chr6:102114780-102119829	Enhancers Weak transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9485528	POU3F2	cis	parietal	SCAN
rs9485528	PRDM13	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:102113600-102114800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:102113600-102117000	Enhancers	HMEC	breast
3	chr6:102113600-102117600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:102113800-102114800	Enhancers	Muscle Satellite Cultured Cells	--
5	chr6:102113800-102114800	Enhancers	NH-A	brain
6	chr6:102114000-102114800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:102114000-102114800	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr6:102114000-102114800	Enhancers	Hela-S3	cervix
9	chr6:102114000-102116800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:102114000-102117000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:102114000-102117000	Enhancers	NHEK	skin
12	chr6:102114600-102121600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	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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