Variant report

Variant	rs10117899
Chromosome Location	chr9:72842727-72842728
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10116549	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10125454	0.87[EUR][1000 genomes]
rs10126027	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10780870	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780871	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780924	0.91[EUR][1000 genomes]
rs10868741	0.88[AFR][1000 genomes]
rs10868742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1112937	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11141917	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142242	0.84[AFR][1000 genomes]
rs11142348	1.00[ASN][1000 genomes]
rs11142365	0.91[EUR][1000 genomes]
rs11142375	0.88[ASN][1000 genomes]
rs11142379	0.91[EUR][1000 genomes]
rs11142380	0.91[EUR][1000 genomes]
rs11142381	0.91[EUR][1000 genomes]
rs1180079	0.84[AFR][1000 genomes]
rs1180081	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180083	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180086	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180087	0.90[AFR][1000 genomes]
rs1180088	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180091	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180094	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180098	0.90[AFR][1000 genomes]
rs1180099	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180101	0.84[AFR][1000 genomes]
rs1180103	0.84[AFR][1000 genomes]
rs1180104	0.88[AFR][1000 genomes]
rs1180106	0.90[AFR][1000 genomes]
rs1180107	0.84[AFR][1000 genomes]
rs1180110	0.93[EUR][1000 genomes]
rs1180111	0.93[EUR][1000 genomes]
rs1180112	0.86[AFR][1000 genomes]
rs1180118	0.81[AFR][1000 genomes]
rs1180126	0.82[AFR][1000 genomes]
rs1180127	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180128	0.82[AFR][1000 genomes]
rs12115787	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12349698	0.90[AMR][1000 genomes]
rs12377677	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051515	0.80[ASN][1000 genomes]
rs17454349	0.80[ASN][1000 genomes]
rs17454433	0.80[ASN][1000 genomes]
rs17526808	0.80[ASN][1000 genomes]
rs1887451	0.87[EUR][1000 genomes]
rs1927096	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927098	0.82[AFR][1000 genomes]
rs1927100	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927101	0.80[ASN][1000 genomes]
rs1927118	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1927124	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927130	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927132	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927133	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927134	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927135	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927136	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1927144	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1986067	0.89[ASN][1000 genomes]
rs2148857	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148859	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148863	0.87[EUR][1000 genomes]
rs2148866	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2148867	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182734	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182735	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182737	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182738	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182741	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309634	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309644	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2479033	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2768643	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2768644	0.84[AFR][1000 genomes]
rs2768645	0.89[AFR][1000 genomes]
rs2768646	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2773362	0.84[AFR][1000 genomes]
rs2773363	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773366	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4384045	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744591	0.92[AFR][1000 genomes]
rs4744989	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4744993	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744999	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5019539	0.80[ASN][1000 genomes]
rs6560015	0.80[ASN][1000 genomes]
rs6560016	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6560018	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66524845	0.92[ASN][1000 genomes]
rs66756859	1.00[ASN][1000 genomes]
rs68171482	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7019147	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020447	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024117	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024812	0.80[ASN][1000 genomes]
rs7034322	0.86[AFR][1000 genomes]
rs7041843	0.82[AFR][1000 genomes]
rs7047789	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7853298	0.87[EUR][1000 genomes]
rs7854735	0.88[AFR][1000 genomes]
rs7860729	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7868564	0.92[AFR][1000 genomes]
rs7869429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871674	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs943534	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047862	chr9:72746875-73138287	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72821200-72844800	Weak transcription	HMEC	breast
2	chr9:72827600-72843200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr9:72828000-72844000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:72828000-72858800	Weak transcription	Gastric	stomach
5	chr9:72828200-72843200	Weak transcription	Fetal Lung	lung
6	chr9:72828200-72844000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr9:72828600-72843000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr9:72829600-72843400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr9:72830800-72845200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr9:72832400-72848800	Weak transcription	Lung	lung
11	chr9:72833600-72856800	Weak transcription	Aorta	Aorta
12	chr9:72834400-72843800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr9:72834600-72844000	Weak transcription	Left Ventricle	heart
14	chr9:72835600-72843200	Weak transcription	Ovary	ovary
15	chr9:72835800-72843200	Weak transcription	Fetal Muscle Leg	muscle
16	chr9:72837200-72847200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:72837800-72843200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr9:72837800-72844000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:72838200-72843600	Weak transcription	Osteobl	bone
20	chr9:72839800-72844800	Weak transcription	HSMMtube	muscle
21	chr9:72840400-72843200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr9:72840400-72844000	Weak transcription	HSMM	muscle
23	chr9:72841200-72843800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr9:72841400-72843400	Weak transcription	Colon Smooth Muscle	Colon
25	chr9:72841400-72844200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:72841600-72843200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr9:72841600-72843200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr9:72842400-72843000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:72842600-72843600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:72842600-72844000	Weak transcription	Right Ventricle	heart
31	chr9:72842600-72844600	Enhancers	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links