Variant report

Variant	rs9825542
Chromosome Location	chr3:180041635-180041636
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10513775	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11923122	1.00[EUR][1000 genomes]
rs13320643	1.00[EUR][1000 genomes]
rs13324315	1.00[EUR][1000 genomes]
rs13327114	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13327183	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1543266	1.00[EUR][1000 genomes]
rs16831253	1.00[EUR][1000 genomes]
rs16831270	1.00[EUR][1000 genomes]
rs2090762	0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2091272	0.82[YRI][hapmap]
rs28373443	1.00[EUR][1000 genomes]
rs28377416	1.00[EUR][1000 genomes]
rs28545820	1.00[EUR][1000 genomes]
rs28623139	1.00[EUR][1000 genomes]
rs28701054	1.00[EUR][1000 genomes]
rs28726303	1.00[EUR][1000 genomes]
rs28736488	1.00[EUR][1000 genomes]
rs28758960	1.00[EUR][1000 genomes]
rs2879655	1.00[EUR][1000 genomes]
rs28818282	1.00[EUR][1000 genomes]
rs4499599	1.00[EUR][1000 genomes]
rs4621328	1.00[EUR][1000 genomes]
rs56406807	1.00[EUR][1000 genomes]
rs57727445	1.00[EUR][1000 genomes]
rs60008753	1.00[EUR][1000 genomes]
rs6765080	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6765906	1.00[EUR][1000 genomes]
rs6772673	1.00[EUR][1000 genomes]
rs6776289	1.00[EUR][1000 genomes]
rs6779403	1.00[EUR][1000 genomes]
rs6784007	1.00[EUR][1000 genomes]
rs6800776	0.80[YRI][hapmap]
rs6803803	1.00[EUR][1000 genomes]
rs6804532	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6809894	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73883804	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73883810	1.00[EUR][1000 genomes]
rs73883833	1.00[EUR][1000 genomes]
rs73885453	1.00[EUR][1000 genomes]
rs73885465	1.00[EUR][1000 genomes]
rs73885473	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73885486	0.80[AFR][1000 genomes]
rs73885496	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7612350	1.00[EUR][1000 genomes]
rs7614651	1.00[EUR][1000 genomes]
rs7628443	1.00[EUR][1000 genomes]
rs7635460	1.00[EUR][1000 genomes]
rs7643125	1.00[EUR][1000 genomes]
rs7646970	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9290693	1.00[EUR][1000 genomes]
rs9290694	1.00[EUR][1000 genomes]
rs9290698	1.00[EUR][1000 genomes]
rs9815044	1.00[EUR][1000 genomes]
rs9819315	1.00[EUR][1000 genomes]
rs9825264	1.00[EUR][1000 genomes]
rs9826576	1.00[EUR][1000 genomes]
rs9827331	1.00[EUR][1000 genomes]
rs9828833	1.00[EUR][1000 genomes]
rs9830454	1.00[EUR][1000 genomes]
rs9832076	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9833910	1.00[EUR][1000 genomes]
rs9836941	1.00[EUR][1000 genomes]
rs9841642	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9841905	1.00[EUR][1000 genomes]
rs9842405	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9844266	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9846836	1.00[EUR][1000 genomes]
rs9849568	1.00[EUR][1000 genomes]
rs9852228	1.00[EUR][1000 genomes]
rs9856995	1.00[EUR][1000 genomes]
rs9861136	1.00[EUR][1000 genomes]
rs9863397	1.00[EUR][1000 genomes]
rs9863949	1.00[EUR][1000 genomes]
rs9866861	1.00[EUR][1000 genomes]
rs9872323	1.00[EUR][1000 genomes]
rs9872365	1.00[EUR][1000 genomes]
rs9873559	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9882377	1.00[EUR][1000 genomes]
rs9884094	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012271	chr3:179806875-180234871	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv878040	chr3:179823887-180128288	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv997388	chr3:179899279-180172349	Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv536817	chr3:179899279-180172349	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv878041	chr3:179983857-180097855	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:180039000-180047400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:180041600-180046800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links