Variant report

Variant	rs9534923
Chromosome Location	chr13:48592723-48592724
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 150 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs1041070	0.87[ASN][1000 genomes]
rs1098354	0.82[ASN][1000 genomes]
rs11148099	0.83[ASN][1000 genomes]
rs11148100	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11618397	0.84[ASN][1000 genomes]
rs1185727	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1326135	0.89[ASN][1000 genomes]
rs1326136	0.84[ASN][1000 genomes]
rs1326140	0.81[ASN][1000 genomes]
rs1536301	0.84[ASN][1000 genomes]
rs1544078	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17071168	0.85[ASN][1000 genomes]
rs1853929	0.80[ASN][1000 genomes]
rs1886975	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1926089	0.84[ASN][1000 genomes]
rs2031590	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2094194	0.86[ASN][1000 genomes]
rs2148243	0.88[ASN][1000 genomes]
rs2148244	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2148245	0.84[ASN][1000 genomes]
rs2182376	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2296574	0.89[ASN][1000 genomes]
rs2406693	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2406697	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2406698	0.86[ASN][1000 genomes]
rs2406699	0.82[ASN][1000 genomes]
rs4245347	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4447314	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4522322	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4941621	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4942725	0.82[ASN][1000 genomes]
rs4942726	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4942727	0.83[ASN][1000 genomes]
rs4942728	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4942729	0.88[ASN][1000 genomes]
rs4942730	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4942735	0.89[ASN][1000 genomes]
rs4942739	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61973260	0.84[EUR][1000 genomes]
rs6561417	0.84[ASN][1000 genomes]
rs6561419	0.88[ASN][1000 genomes]
rs6561420	0.88[ASN][1000 genomes]
rs6561424	0.89[ASN][1000 genomes]
rs6561427	0.88[ASN][1000 genomes]
rs6561430	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6561431	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6561432	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs718010	0.84[ASN][1000 genomes]
rs7318770	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7319245	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7320366	0.86[ASN][1000 genomes]
rs7320461	0.84[ASN][1000 genomes]
rs7320759	0.84[ASN][1000 genomes]
rs7322515	0.88[ASN][1000 genomes]
rs7325189	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7325437	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7326889	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7326984	0.88[ASN][1000 genomes]
rs7327730	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7328525	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7328537	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7329419	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7330130	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7330472	0.82[AFR][1000 genomes]
rs7330913	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7331285	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7331900	0.81[AFR][1000 genomes]
rs7332304	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7333659	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7333821	0.84[ASN][1000 genomes]
rs7334207	0.84[ASN][1000 genomes]
rs7335788	0.84[ASN][1000 genomes]
rs7336972	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7337004	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7337744	0.89[ASN][1000 genomes]
rs7338125	0.84[ASN][1000 genomes]
rs7338373	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7338894	0.83[ASN][1000 genomes]
rs765809	0.84[ASN][1000 genomes]
rs7989231	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7990244	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7990266	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7990505	0.88[ASN][1000 genomes]
rs7994359	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7996580	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7997802	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7998116	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7998260	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7998497	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7998998	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7999505	0.80[ASN][1000 genomes]
rs8000164	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8001432	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8001871	0.81[AFR][1000 genomes]
rs9316339	0.86[ASN][1000 genomes]
rs9316343	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9316344	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9526417	0.81[ASN][1000 genomes]
rs9526422	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9526423	0.84[ASN][1000 genomes]
rs9526426	0.84[ASN][1000 genomes]
rs9526429	0.89[ASN][1000 genomes]
rs9526430	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9526433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526434	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9534876	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9534877	0.84[ASN][1000 genomes]
rs9534878	0.84[ASN][1000 genomes]
rs9534879	0.84[ASN][1000 genomes]
rs9534880	0.84[ASN][1000 genomes]
rs9534882	0.83[ASN][1000 genomes]
rs9534885	0.84[ASN][1000 genomes]
rs9534889	0.88[ASN][1000 genomes]
rs9534892	0.86[ASN][1000 genomes]
rs9534896	0.85[ASN][1000 genomes]
rs9534897	0.82[ASN][1000 genomes]
rs9534898	0.89[ASN][1000 genomes]
rs9534901	0.89[ASN][1000 genomes]
rs9534903	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9534904	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9534905	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9534906	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9534907	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9534908	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9534909	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9534912	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9534913	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9534918	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9534919	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9534922	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9534926	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9534929	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9562787	0.84[ASN][1000 genomes]
rs9567954	0.87[ASN][1000 genomes]
rs9567955	0.87[ASN][1000 genomes]
rs9567958	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9567959	0.84[ASN][1000 genomes]
rs9567960	0.84[ASN][1000 genomes]
rs9567963	0.84[ASN][1000 genomes]
rs9567964	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9567972	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9567976	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9567979	0.84[AFR][1000 genomes]
rs9567980	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9567986	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9595815	0.86[ASN][1000 genomes]
rs9595825	0.84[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	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv974089	chr13:48588484-48594798	Enhancers Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9534923	SUCLA2	Cis_1M	lymphoblastoid	RTeQTL
rs9534923	SUCLA2	cis	Muscle Skeletal	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48576000-48603600	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr13:48576000-48604000	Weak transcription	Primary T cells from cord blood	blood
3	chr13:48576000-48604800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr13:48576000-48604800	Weak transcription	Fetal Stomach	stomach
5	chr13:48576000-48604800	Weak transcription	Thymus	Thymus
6	chr13:48576000-48610800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr13:48576000-48611400	Weak transcription	Left Ventricle	heart
8	chr13:48576400-48605000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr13:48576600-48604800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr13:48576600-48604800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr13:48576600-48604800	Weak transcription	Dnd41	blood
12	chr13:48576600-48610200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr13:48583400-48592800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr13:48583800-48604600	Weak transcription	Liver	Liver
15	chr13:48584000-48604600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr13:48584000-48610800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr13:48584200-48604800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr13:48584200-48611200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr13:48584400-48592800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr13:48584400-48604600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr13:48584800-48604800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr13:48586000-48603800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr13:48587400-48604000	Weak transcription	Primary B cells from cord blood	blood
24	chr13:48588000-48603800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr13:48588600-48605800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr13:48588800-48605200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr13:48589000-48604800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr13:48589200-48605200	Weak transcription	Fetal Intestine Large	intestine
29	chr13:48592400-48593200	Enhancers	Stomach Mucosa	stomach
30	chr13:48592400-48604800	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links