Variant report

Variant	rs11042623
Chromosome Location	chr11:10117334-10117335
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 125 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10743129	0.81[EUR][1000 genomes]
rs10770103	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840325	1.00[CHB][hapmap]
rs10840327	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs10840330	0.83[CEU][hapmap]
rs10840333	0.83[CEU][hapmap]
rs10840334	0.84[CEU][hapmap]
rs10840337	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840338	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840344	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840359	0.91[EUR][1000 genomes]
rs10840375	0.84[EUR][1000 genomes]
rs10840377	1.00[CEU][hapmap]
rs11042543	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.80[TSI][hapmap]
rs11042550	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs11042556	1.00[CHB][hapmap]
rs11042559	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs11042561	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs11042571	0.83[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042578	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042579	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042580	0.81[EUR][1000 genomes]
rs11042593	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042595	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042615	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042627	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042632	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11042641	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11042721	0.80[CEU][hapmap]
rs11600251	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11600489	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11602515	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs11603440	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606561	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11607682	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607703	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12360783	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12362060	0.95[CEU][hapmap]
rs12362938	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12364676	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12416695	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12417184	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12418212	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12418514	1.00[ASN][1000 genomes]
rs12418619	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12419564	1.00[CHB][hapmap]
rs12419923	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12420122	0.83[EUR][1000 genomes]
rs12420734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12420950	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12421179	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421200	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421931	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372807	0.90[CEU][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes]
rs1372808	0.82[EUR][1000 genomes]
rs1442737	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17270804	1.00[CHB][hapmap]
rs17271847	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17355675	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap]
rs17355924	1.00[CHB][hapmap]
rs17356792	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17359113	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1822291	0.83[EUR][1000 genomes]
rs1822292	0.95[CEU][hapmap];0.91[TSI][hapmap]
rs1867135	0.84[EUR][1000 genomes]
rs2197171	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2403227	0.84[CEU][hapmap]
rs2403229	0.84[CEU][hapmap]
rs2403292	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs28731164	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34683105	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4271380	0.83[EUR][1000 genomes]
rs4281477	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4385889	0.83[EUR][1000 genomes]
rs4450168	1.00[ASN][1000 genomes]
rs4478985	0.91[EUR][1000 genomes]
rs4519084	0.83[EUR][1000 genomes]
rs4529876	0.92[EUR][1000 genomes]
rs4576815	0.84[CEU][hapmap]
rs4625455	0.90[CEU][hapmap]
rs4643073	0.81[EUR][1000 genomes]
rs4909915	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs4909917	0.84[CEU][hapmap]
rs4910075	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap]
rs4910080	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs4910081	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap]
rs4910084	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4910086	0.84[CEU][hapmap]
rs4910095	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4910098	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55788918	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55796222	0.83[EUR][1000 genomes]
rs56853694	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61877048	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61877049	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61878582	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61878587	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61878622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61878636	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61889838	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7114303	0.90[CEU][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs7123453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7123820	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131445	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7924875	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7928959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7931804	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935774	0.84[EUR][1000 genomes]
rs7935934	1.00[CEU][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7938491	1.00[CEU][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7938502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938788	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs7945980	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7946995	0.90[EUR][1000 genomes]
rs7947306	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7948215	0.85[EUR][1000 genomes]
rs7950447	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv553476	chr11:10024311-10117435	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11042623	OR52B2	cis	parietal	SCAN
rs11042623	OR10A5	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10098600-10121800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:10110400-10121800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr11:10110400-10122200	Weak transcription	HSMM	muscle
4	chr11:10112000-10119200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:10112400-10122000	Weak transcription	NHLF	lung
6	chr11:10113200-10119200	Weak transcription	Fetal Brain Male	brain
7	chr11:10113400-10118600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr11:10113400-10119400	Weak transcription	Fetal Lung	lung
9	chr11:10113800-10118400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr11:10114000-10118600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr11:10114000-10123200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr11:10114400-10118600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr11:10114800-10120000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr11:10116800-10118400	Enhancers	Hela-S3	cervix
15	chr11:10116800-10125400	Weak transcription	Ovary	ovary
16	chr11:10116800-10131000	Weak transcription	Gastric	stomach
17	chr11:10117000-10117400	Flanking Active TSS	A549	lung
18	chr11:10117000-10117600	Enhancers	Muscle Satellite Cultured Cells	--
19	chr11:10117200-10117600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr11:10117200-10131000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links