Variant report

Variant	rs2896513
Chromosome Location	chr11:10027543-10027544
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 119 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10160247	0.86[JPT][hapmap]
rs10160669	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs10500716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10500719	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs10500720	0.90[JPT][hapmap]
rs10500721	0.82[JPT][hapmap]
rs11042575	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs11042586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11042602	0.82[ASN][1000 genomes]
rs11042656	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs11042657	0.85[JPT][hapmap]
rs11042664	0.86[JPT][hapmap]
rs11042666	0.89[CHD][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap]
rs11821308	0.85[JPT][hapmap]
rs11825114	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12274104	0.86[JPT][hapmap]
rs12278735	0.86[JPT][hapmap]
rs12281526	0.86[JPT][hapmap]
rs12286927	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs12287386	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs12288200	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs12288275	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs12288486	0.86[JPT][hapmap]
rs12288654	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs12576008	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs1442736	0.86[JPT][hapmap]
rs16907329	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs16907334	0.94[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16907407	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16907410	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16907417	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16907462	0.86[JPT][hapmap]
rs16907471	0.85[JPT][hapmap]
rs16907481	0.97[CHD][hapmap];0.86[JPT][hapmap];0.93[MEX][hapmap]
rs16907493	0.97[CHD][hapmap];0.86[JPT][hapmap]
rs16907504	0.86[JPT][hapmap];0.85[AMR][1000 genomes]
rs16907533	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs16907561	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs16907568	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs2028576	0.85[JPT][hapmap]
rs2069214	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs2119991	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs2278630	0.86[JPT][hapmap]
rs2278632	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs2278633	0.89[JPT][hapmap]
rs2278634	0.86[JPT][hapmap]
rs2403261	0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2403263	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2403267	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2896514	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2896515	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2896517	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3178898	0.86[JPT][hapmap]
rs34984386	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35815123	0.82[AMR][1000 genomes]
rs4323860	0.82[JPT][hapmap]
rs4910090	0.93[CHB][hapmap];0.95[JPT][hapmap]
rs4910091	0.81[ASN][1000 genomes]
rs4910092	0.94[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56850765	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57180563	0.80[ASN][1000 genomes]
rs58652557	0.82[AMR][1000 genomes]
rs58842960	0.83[ASN][1000 genomes]
rs59479500	0.92[ASN][1000 genomes]
rs60257382	0.82[AMR][1000 genomes]
rs61877010	0.80[EUR][1000 genomes]
rs61877012	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61877018	0.91[ASN][1000 genomes]
rs61877040	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61877043	0.84[ASN][1000 genomes]
rs61877045	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61878580	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61878581	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61878584	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61878585	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61878625	0.80[AMR][1000 genomes]
rs6483969	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs67132348	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7103902	0.93[JPT][hapmap]
rs7105321	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7106234	0.88[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7107021	0.81[JPT][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs7107302	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs7107916	0.88[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7113715	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7121157	0.81[ASN][1000 genomes]
rs7122422	0.92[YRI][hapmap]
rs7123728	0.82[JPT][hapmap]
rs7124925	0.90[JPT][hapmap];0.84[YRI][hapmap]
rs7128234	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7128838	0.89[ASN][1000 genomes]
rs7129047	0.86[JPT][hapmap]
rs7130610	0.87[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs713402	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs721008	0.86[JPT][hapmap]
rs7479039	0.82[JPT][hapmap]
rs7925889	0.88[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7926141	0.82[ASN][1000 genomes]
rs7926678	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7930920	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7931957	0.82[ASN][1000 genomes]
rs7932484	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7935297	0.87[ASN][1000 genomes]
rs7936409	0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7936461	0.83[ASN][1000 genomes]
rs7938534	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7938932	0.82[ASN][1000 genomes]
rs7939064	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7940348	0.90[ASN][1000 genomes]
rs7946649	0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7949164	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7949322	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9645625	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs9888170	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][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	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	nsv896989	chr11:9951968-10059623	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv553475	chr11:10019879-10059623	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	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
5	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
rs2896513	OR10A4	cis	cerebellum	SCAN
rs2896513	BTBD10	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9981400-10051600	Weak transcription	Aorta	Aorta
2	chr11:9985800-10049000	Weak transcription	Left Ventricle	heart
3	chr11:9990400-10028200	Weak transcription	Fetal Brain Female	brain
4	chr11:9991200-10060000	Weak transcription	Colon Smooth Muscle	Colon
5	chr11:9994800-10041800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr11:10001400-10066200	Weak transcription	Pancreas	Pancrea
7	chr11:10004200-10048600	Weak transcription	Brain Angular Gyrus	brain
8	chr11:10004600-10027600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr11:10005200-10027600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:10005400-10027600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:10005400-10029000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:10007600-10041800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr11:10010600-10030000	Weak transcription	Primary T cells from cord blood	blood
14	chr11:10010600-10051200	Weak transcription	Ovary	ovary
15	chr11:10011600-10028000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:10012600-10049000	Weak transcription	Fetal Kidney	kidney
17	chr11:10018000-10031400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:10020400-10027600	Weak transcription	Fetal Lung	lung
19	chr11:10021000-10031400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr11:10021800-10030200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr11:10022600-10027800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr11:10022600-10032400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr11:10023800-10033400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr11:10024200-10047800	Weak transcription	Osteobl	bone
25	chr11:10024600-10041600	Weak transcription	HUVEC	blood vessel
26	chr11:10024800-10054000	Weak transcription	Hela-S3	cervix
27	chr11:10026200-10030000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
28	chr11:10026400-10028200	Enhancers	Placenta	Placenta
29	chr11:10026600-10030000	Weak transcription	HSMMtube	muscle
30	chr11:10026600-10030400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr11:10026800-10030200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:10027000-10028800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:10027200-10027800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
34	chr11:10027200-10028000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:10027200-10028000	ZNF genes & repeats	A549	lung
36	chr11:10027200-10028400	ZNF genes & repeats	Fetal Intestine Small	intestine
37	chr11:10027200-10028800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
38	chr11:10027200-10028800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr11:10027200-10028800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr11:10027200-10029200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr11:10027200-10029400	ZNF genes & repeats	Fetal Muscle Leg	muscle
42	chr11:10027200-10030400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:10027400-10027600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:10027400-10027600	Strong transcription	Fetal Stomach	stomach
45	chr11:10027400-10028200	Active TSS	Adipose Nuclei	Adipose
46	chr11:10027400-10030000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr11:10027400-10030000	ZNF genes & repeats	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links