Variant report

Variant	rs10509565
Chromosome Location	chr10:90889108-90889109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10509564	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10887906	0.86[ASN][1000 genomes]
rs10887913	1.00[ASN][1000 genomes]
rs11202956	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11202968	0.99[ASN][1000 genomes]
rs11202971	0.99[ASN][1000 genomes]
rs11202973	0.96[ASN][1000 genomes]
rs11202974	0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11202978	0.96[ASN][1000 genomes]
rs11202984	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11202986	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11202987	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11202990	1.00[ASN][1000 genomes]
rs11202991	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11202992	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11202995	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11202996	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];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12359686	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1344234	0.85[ASN][1000 genomes]
rs17378555	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17378695	0.82[YRI][hapmap]
rs17378702	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs17380509	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17380676	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17463822	0.99[ASN][1000 genomes]
rs17464831	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17464997	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17465248	1.00[ASN][1000 genomes]
rs1937324	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2154249	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2154250	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2256329	0.86[ASN][1000 genomes]
rs2494647	0.85[ASN][1000 genomes]
rs28461567	1.00[ASN][1000 genomes]
rs28533190	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2863221	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2902448	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7094057	0.99[ASN][1000 genomes]
rs72810981	0.92[ASN][1000 genomes]
rs72810994	0.99[ASN][1000 genomes]
rs72812827	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72812830	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72812831	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72812833	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72812834	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72812845	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72812848	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72812849	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72812851	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72812855	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72812859	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72812860	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72812862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72812886	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72812889	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72812894	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7896854	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv467416	chr10:90815975-90889997	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv551842	chr10:90815975-90889997	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv831944	chr10:90822654-90967018	Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	esv2758235	chr10:90835064-91017486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv2759775	chr10:90835064-91017486	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv895881	chr10:90842431-90940003	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1041964	chr10:90861380-91378356	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
10	nsv551844	chr10:90879304-90899444	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10509565	MINPP1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90878400-90889600	Weak transcription	NHLF	lung
2	chr10:90882400-90889200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr10:90884200-90889200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr10:90888000-90890400	Enhancers	NHDF-Ad	bronchial
5	chr10:90888400-90889600	Weak transcription	HMEC	breast
6	chr10:90888600-90889400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr10:90888600-90889600	Weak transcription	NHEK	skin
8	chr10:90889000-90889600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links