Variant report

Variant	rs16907407
Chromosome Location	chr11:10056305-10056306
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10160247	0.83[CHB][hapmap]
rs10160669	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs10500716	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10500719	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs10500723	0.92[CHD][hapmap]
rs11042575	0.88[CHB][hapmap];0.95[YRI][hapmap]
rs11042586	0.94[CHB][hapmap]
rs11042656	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs11042664	0.83[CHB][hapmap]
rs11042666	0.83[CHB][hapmap];0.89[CHD][hapmap];0.85[MEX][hapmap]
rs11825114	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12274104	0.83[CHB][hapmap]
rs12278680	0.83[CHB][hapmap];0.91[CHD][hapmap]
rs12278735	0.83[CHB][hapmap]
rs12281526	0.83[CHB][hapmap]
rs12286927	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs12287386	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs12288200	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs12288275	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs12288486	0.83[CHB][hapmap]
rs12288654	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs12576008	0.94[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs1442736	0.83[CHB][hapmap]
rs16907329	0.94[CHB][hapmap]
rs16907334	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16907410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16907417	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16907462	0.82[CHB][hapmap];0.80[AMR][1000 genomes]
rs16907471	0.83[CHB][hapmap]
rs16907481	0.83[CHB][hapmap];0.92[CHD][hapmap];0.93[MEX][hapmap];0.80[AMR][1000 genomes]
rs16907493	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs16907504	0.83[CHB][hapmap];0.87[AMR][1000 genomes]
rs16907533	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs16907561	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs16907568	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs1822294	0.83[CHB][hapmap]
rs1822295	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs1867137	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs1867138	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs2028576	0.83[CHB][hapmap]
rs2069214	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs2119991	0.92[CHD][hapmap]
rs2278630	0.83[CHB][hapmap]
rs2278632	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs2278633	0.83[CHB][hapmap]
rs2403261	0.81[ASW][hapmap];0.81[CHB][hapmap]
rs2403263	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2403267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2896513	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]
rs2896514	0.87[CHB][hapmap]
rs2896515	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2896517	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3178898	0.83[CHB][hapmap]
rs34984386	0.80[AMR][1000 genomes]
rs35815123	0.80[AMR][1000 genomes]
rs4910090	1.00[CHB][hapmap]
rs4910092	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56850765	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57618276	0.80[AMR][1000 genomes]
rs58652557	0.80[AMR][1000 genomes]
rs59479500	0.82[ASN][1000 genomes]
rs60257382	0.80[AMR][1000 genomes]
rs61520995	0.80[AMR][1000 genomes]
rs61877012	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61877018	0.86[AFR][1000 genomes]
rs61877040	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61877043	0.80[ASN][1000 genomes]
rs61877045	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61878580	0.82[AMR][1000 genomes]
rs61878581	0.82[AMR][1000 genomes]
rs61878584	0.80[AMR][1000 genomes]
rs61878585	0.80[AMR][1000 genomes]
rs61878625	0.82[AMR][1000 genomes]
rs61878628	0.80[AMR][1000 genomes]
rs61878631	0.80[AMR][1000 genomes]
rs61878634	0.80[AMR][1000 genomes]
rs6483969	0.80[AMR][1000 genomes]
rs67132348	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67404901	0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7103902	0.89[CHB][hapmap]
rs7105321	0.80[AMR][1000 genomes]
rs7106234	0.94[CHB][hapmap]
rs7107302	0.94[CHB][hapmap]
rs7107916	1.00[ASW][hapmap];0.94[CHB][hapmap];0.82[LWK][hapmap]
rs7113715	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7124925	0.80[AMR][1000 genomes]
rs7128234	0.94[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7129047	0.83[CHB][hapmap];0.80[AMR][1000 genomes]
rs7130610	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs713402	0.94[CHB][hapmap]
rs721008	0.83[CHB][hapmap]
rs72860548	0.80[AMR][1000 genomes]
rs7925889	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs7930920	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7932484	0.87[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs7935297	0.86[AFR][1000 genomes]
rs7936409	0.82[CHB][hapmap];0.80[AMR][1000 genomes]
rs7938534	0.80[AMR][1000 genomes]
rs7939064	0.80[AMR][1000 genomes]
rs7940348	0.83[AFR][1000 genomes]
rs7946649	0.83[CHB][hapmap];0.80[AMR][1000 genomes]
rs7949164	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7949322	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9888170	0.94[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap];0.84[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
rs16907407	BTBD10	cis	parietal	SCAN
rs16907407	OR10A4	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9991200-10060000	Weak transcription	Colon Smooth Muscle	Colon
2	chr11:10001400-10066200	Weak transcription	Pancreas	Pancrea
3	chr11:10030600-10065800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:10035200-10065800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr11:10036200-10062800	Weak transcription	Adipose Nuclei	Adipose
6	chr11:10040400-10065800	Weak transcription	HSMM	muscle
7	chr11:10042200-10064400	Weak transcription	Fetal Intestine Small	intestine
8	chr11:10042200-10066000	Weak transcription	Fetal Muscle Leg	muscle
9	chr11:10042200-10066000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr11:10042200-10066200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:10042600-10066000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr11:10043400-10065600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr11:10043800-10061000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr11:10043800-10063800	Weak transcription	Primary T cells from cord blood	blood
15	chr11:10043800-10065400	Weak transcription	A549	lung
16	chr11:10043800-10065600	Weak transcription	HepG2	liver
17	chr11:10046400-10065800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr11:10046400-10065800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr11:10048600-10064600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr11:10048800-10061200	Weak transcription	HUVEC	blood vessel
21	chr11:10049200-10063200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr11:10049200-10065000	Weak transcription	Dnd41	blood
23	chr11:10049400-10065600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr11:10049800-10065000	Weak transcription	Fetal Intestine Large	intestine
25	chr11:10049800-10065600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr11:10049800-10066000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr11:10049800-10066000	Weak transcription	Fetal Kidney	kidney
28	chr11:10050200-10059000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr11:10050200-10066000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:10050200-10066800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr11:10050600-10064200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:10050600-10065000	Weak transcription	Placenta	Placenta
33	chr11:10051400-10057200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:10051400-10062200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr11:10051400-10063400	Weak transcription	Liver	Liver
36	chr11:10052000-10062600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr11:10053200-10056600	Enhancers	NHDF-Ad	bronchial
38	chr11:10054200-10063200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr11:10054600-10059600	Weak transcription	Fetal Lung	lung
40	chr11:10055200-10059600	Weak transcription	Hela-S3	cervix
41	chr11:10055400-10059800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr11:10055600-10060000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr11:10055800-10060000	Weak transcription	Osteobl	bone
44	chr11:10056000-10059200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr11:10056000-10061000	Weak transcription	NHLF	lung
46	chr11:10056000-10063200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:10056200-10058400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr11:10056200-10063800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr11:10056200-10066000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links