Variant report

Variant	rs7935934
Chromosome Location	chr11:10201185-10201186
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:10200393..10205018-chr11:10324375..10327775,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254554	Chromatin interaction
ENSG00000148926	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10770103	0.94[EUR][1000 genomes]
rs10840359	0.82[EUR][1000 genomes]
rs10840375	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10840377	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11042593	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11042595	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11042601	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11042609	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11042615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11042618	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11042623	1.00[CEU][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11042627	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11042632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11042641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11042683	1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11042721	0.82[CEU][hapmap]
rs11600251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11600489	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11606561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11607682	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11607703	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12360783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12362060	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12362938	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12364676	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12416695	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12417184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12418212	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12418619	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12420122	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12420734	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12421096	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12421179	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12421931	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13306112	1.00[YRI][hapmap]
rs1372807	0.91[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs1372808	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1372811	1.00[CHB][hapmap]
rs1442737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1470258	1.00[YRI][hapmap]
rs1562782	0.85[CHD][hapmap]
rs17359113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1822291	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1822292	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1822293	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1867135	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2044142	0.83[CHD][hapmap]
rs2044146	0.88[YRI][hapmap]
rs2083712	0.88[YRI][hapmap]
rs2083713	0.88[YRI][hapmap]
rs2197171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2403292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28731164	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2920154	0.88[YRI][hapmap]
rs2957657	0.83[CHD][hapmap]
rs34683105	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4271380	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4281477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4385889	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4478985	0.80[EUR][1000 genomes]
rs4519084	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4529876	0.81[EUR][1000 genomes]
rs4625455	0.91[CEU][hapmap]
rs4643073	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4910093	0.88[YRI][hapmap]
rs4910095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910098	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4910111	1.00[CHB][hapmap]
rs55788918	0.94[EUR][1000 genomes]
rs55796222	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56853694	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61877048	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61877049	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61878582	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61878587	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61878622	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61878636	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61889838	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7104093	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs7110151	1.00[CHB][hapmap]
rs7114303	0.91[CEU][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs7123453	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7123820	0.87[EUR][1000 genomes]
rs7124401	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7924875	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7928959	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7931804	0.83[AMR][1000 genomes]
rs7935774	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7938491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7938502	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7938647	1.00[CEU][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7938788	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs7945980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7946995	0.81[EUR][1000 genomes]
rs7947306	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7948215	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7950447	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]

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	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv1039636	chr11:10126747-10280570	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1036041	chr11:10131018-10212202	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7935934	OR10A5	cis	cerebellum	SCAN
rs7935934	OR52B2	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10178200-10213400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:10184600-10211400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr11:10186200-10209200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr11:10188000-10222800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:10194800-10206800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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