Variant report

Variant	rs9852406
Chromosome Location	chr3:135625498-135625499
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10048942	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs10049233	0.81[AMR][1000 genomes]
rs10512981	1.00[JPT][hapmap]
rs10512990	0.94[CEU][hapmap]
rs10935175	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13079205	0.95[CEU][hapmap]
rs13082684	0.81[AMR][1000 genomes]
rs13097248	0.88[CEU][hapmap]
rs13097946	1.00[JPT][hapmap]
rs13098245	1.00[JPT][hapmap]
rs13325914	1.00[JPT][hapmap]
rs13434196	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1403763	0.95[CEU][hapmap]
rs1403767	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1403770	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs16843509	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17197552	1.00[JPT][hapmap]
rs28576629	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28875187	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56308637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6771997	1.00[JPT][hapmap]
rs6774289	1.00[JPT][hapmap]
rs6775778	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6792630	0.94[CEU][hapmap]
rs6793835	0.95[CEU][hapmap]
rs6799056	0.89[CEU][hapmap]
rs6799320	0.84[CEU][hapmap]
rs6802139	1.00[JPT][hapmap]
rs6807058	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6807242	1.00[JPT][hapmap]
rs6809006	1.00[JPT][hapmap]
rs7621331	1.00[JPT][hapmap]
rs7621396	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7621425	1.00[JPT][hapmap]
rs7628848	0.81[AMR][1000 genomes]
rs7638129	1.00[JPT][hapmap]
rs7643661	1.00[JPT][hapmap]
rs9289503	1.00[JPT][hapmap]
rs9653930	0.95[CEU][hapmap]
rs9808979	1.00[JPT][hapmap]
rs9812561	1.00[JPT][hapmap]
rs9814557	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9825239	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9826806	1.00[JPT][hapmap]
rs9827662	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9829329	1.00[JPT][hapmap]
rs9829476	1.00[JPT][hapmap]
rs9834624	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9836374	1.00[JPT][hapmap]
rs9836758	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9839259	1.00[JPT][hapmap]
rs9842840	1.00[JPT][hapmap]
rs9843725	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9844478	1.00[JPT][hapmap]
rs9848322	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9848926	0.95[CEU][hapmap]
rs9849088	1.00[JPT][hapmap]
rs9853577	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9854494	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9862264	1.00[JPT][hapmap]
rs9864247	1.00[JPT][hapmap]
rs9864656	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9864775	1.00[JPT][hapmap]
rs9870581	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs9872542	1.00[JPT][hapmap]
rs9875948	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs9883808	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv829732	chr3:135561706-135756840	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9852406	MSL2	cis	cerebellum	SCAN
rs9852406	PPP2R3A	cis	cerebellum	SCAN
rs9852406	RNF184	cis	multi-tissue	Pritchard

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135617000-135625600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:135617000-135626000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:135624600-135625800	Weak transcription	NHEK	skin

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