Variant report

Variant	rs3099953
Chromosome Location	chr2:39117618-39117619
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10166557	1.00[EUR][1000 genomes]
rs10173380	1.00[EUR][1000 genomes]
rs10173563	1.00[EUR][1000 genomes]
rs10186842	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10188701	1.00[EUR][1000 genomes]
rs10194533	1.00[EUR][1000 genomes]
rs10202876	1.00[EUR][1000 genomes]
rs10203565	1.00[EUR][1000 genomes]
rs10495882	1.00[EUR][1000 genomes]
rs12329307	1.00[EUR][1000 genomes]
rs13387231	1.00[EUR][1000 genomes]
rs13394446	1.00[EUR][1000 genomes]
rs13395448	1.00[EUR][1000 genomes]
rs13407659	1.00[EUR][1000 genomes]
rs13424493	1.00[EUR][1000 genomes]
rs1376461	1.00[JPT][hapmap]
rs1451278	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023148	1.00[EUR][1000 genomes]
rs17023149	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023214	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs17023241	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023292	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17425982	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1901290	1.00[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2218850	1.00[EUR][1000 genomes]
rs2373466	1.00[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2373472	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3099938	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3099947	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3099973	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3099986	1.00[EUR][1000 genomes]
rs3099996	1.00[EUR][1000 genomes]
rs3099997	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112138	1.00[JPT][hapmap]
rs3112145	1.00[EUR][1000 genomes]
rs3112146	1.00[EUR][1000 genomes]
rs3112148	1.00[EUR][1000 genomes]
rs3112155	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3112157	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3112158	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3112160	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs3112164	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112174	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112176	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3112177	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55890805	1.00[EUR][1000 genomes]
rs56322480	1.00[ASN][1000 genomes]
rs57884089	0.92[ASN][1000 genomes]
rs58412684	1.00[ASN][1000 genomes]
rs58645810	1.00[ASN][1000 genomes]
rs59788371	1.00[ASN][1000 genomes]
rs60406386	1.00[ASN][1000 genomes]
rs60703378	1.00[EUR][1000 genomes]
rs61393528	1.00[ASN][1000 genomes]
rs6544182	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6712917	1.00[JPT][hapmap]
rs6722176	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6722478	1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6734212	1.00[EUR][1000 genomes]
rs6737680	1.00[EUR][1000 genomes]
rs6748000	1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6751306	1.00[EUR][1000 genomes]
rs6753426	1.00[EUR][1000 genomes]
rs6754613	1.00[EUR][1000 genomes]
rs718312	1.00[EUR][1000 genomes]
rs72906436	1.00[EUR][1000 genomes]
rs72906467	1.00[EUR][1000 genomes]
rs72916836	1.00[EUR][1000 genomes]
rs72916860	1.00[EUR][1000 genomes]
rs72918710	1.00[EUR][1000 genomes]
rs7340303	1.00[EUR][1000 genomes]
rs7368897	1.00[JPT][hapmap]
rs73930373	1.00[ASN][1000 genomes]
rs73930374	1.00[ASN][1000 genomes]
rs73930378	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7559586	1.00[EUR][1000 genomes]
rs7565814	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7571608	1.00[EUR][1000 genomes]
rs7571719	1.00[EUR][1000 genomes]
rs7571935	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7582586	1.00[EUR][1000 genomes]
rs7583010	1.00[CEU][hapmap]
rs7599990	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7605183	1.00[ASN][1000 genomes]
rs921433	1.00[JPT][hapmap]
rs9646968	1.00[EUR][1000 genomes]
rs9678084	1.00[CEU][hapmap]

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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3099953	SOS1	cis	multi-tissue	Pritchard

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39103800-39120200	Weak transcription	Left Ventricle	heart
2	chr2:39104200-39119400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:39104200-39122200	Weak transcription	Ovary	ovary
4	chr2:39104200-39129000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:39110200-39186800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:39110400-39120600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:39113600-39118800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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