Variant report

Variant	rs4245347
Chromosome Location	chr13:48533936-48533937
allele	A/G
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:148)

rs_ID	r²[population]
rs1041070	0.90[ASN][1000 genomes]
rs11148099	0.83[ASN][1000 genomes]
rs11148100	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11618397	0.91[ASN][1000 genomes]
rs1185727	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12864691	0.86[AFR][1000 genomes]
rs1326135	0.86[ASN][1000 genomes]
rs1326136	0.88[ASN][1000 genomes]
rs1326138	0.87[ASN][1000 genomes]
rs1326139	0.87[ASN][1000 genomes]
rs1326140	0.88[ASN][1000 genomes]
rs1536301	0.84[ASN][1000 genomes]
rs1544078	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17071168	0.82[ASN][1000 genomes]
rs1853929	0.87[ASN][1000 genomes]
rs1886975	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1886976	0.81[ASN][1000 genomes]
rs1926089	0.91[ASN][1000 genomes]
rs2031590	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2031591	0.81[AFR][1000 genomes]
rs2094194	0.89[ASN][1000 genomes]
rs2148243	0.88[ASN][1000 genomes]
rs2148244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2148245	0.91[ASN][1000 genomes]
rs2182376	0.87[ASN][1000 genomes]
rs2296573	0.82[AFR][1000 genomes]
rs2296574	0.86[ASN][1000 genomes]
rs2406693	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2406697	0.87[ASN][1000 genomes]
rs2406698	0.83[ASN][1000 genomes]
rs4447314	0.87[ASN][1000 genomes]
rs4522322	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4941621	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4942725	0.89[ASN][1000 genomes]
rs4942726	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4942727	0.87[ASN][1000 genomes]
rs4942728	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4942729	0.88[ASN][1000 genomes]
rs4942730	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4942735	0.86[ASN][1000 genomes]
rs4942739	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61973260	0.80[EUR][1000 genomes]
rs6561417	0.91[ASN][1000 genomes]
rs6561419	0.88[ASN][1000 genomes]
rs6561420	0.88[ASN][1000 genomes]
rs6561424	0.86[ASN][1000 genomes]
rs6561427	0.85[ASN][1000 genomes]
rs6561430	0.86[ASN][1000 genomes]
rs6561431	0.85[ASN][1000 genomes]
rs6561432	0.85[ASN][1000 genomes]
rs718010	0.91[ASN][1000 genomes]
rs7318770	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7319245	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7320366	0.89[ASN][1000 genomes]
rs7320461	0.91[ASN][1000 genomes]
rs7320759	0.91[ASN][1000 genomes]
rs7322515	0.88[ASN][1000 genomes]
rs7325189	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7325437	0.85[ASN][1000 genomes]
rs7326889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7326984	0.88[ASN][1000 genomes]
rs7327730	0.87[ASN][1000 genomes]
rs7328525	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7328537	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7329419	0.84[ASN][1000 genomes]
rs7330130	0.85[ASN][1000 genomes]
rs7330913	0.86[ASN][1000 genomes]
rs7331285	0.85[ASN][1000 genomes]
rs7332304	0.85[ASN][1000 genomes]
rs7333659	0.83[ASN][1000 genomes]
rs7333821	0.91[ASN][1000 genomes]
rs7334207	0.91[ASN][1000 genomes]
rs7335788	0.91[ASN][1000 genomes]
rs7336972	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7337004	0.85[ASN][1000 genomes]
rs7337744	0.86[ASN][1000 genomes]
rs7338125	0.91[ASN][1000 genomes]
rs7338373	0.85[ASN][1000 genomes]
rs7338894	0.89[ASN][1000 genomes]
rs765809	0.91[ASN][1000 genomes]
rs7985357	0.84[ASN][1000 genomes]
rs7989231	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7990244	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7990266	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7990505	0.88[ASN][1000 genomes]
rs7994359	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7996580	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7997802	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7998116	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7998260	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7998497	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7998998	0.87[ASN][1000 genomes]
rs8000164	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8001432	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8001871	0.85[AFR][1000 genomes]
rs9316339	0.89[ASN][1000 genomes]
rs9316343	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9316344	0.87[ASN][1000 genomes]
rs9526417	0.88[ASN][1000 genomes]
rs9526422	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526423	0.91[ASN][1000 genomes]
rs9526426	0.88[ASN][1000 genomes]
rs9526429	0.86[ASN][1000 genomes]
rs9526430	0.87[ASN][1000 genomes]
rs9526433	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9526434	0.85[ASN][1000 genomes]
rs9534876	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9534877	0.91[ASN][1000 genomes]
rs9534878	0.91[ASN][1000 genomes]
rs9534879	0.91[ASN][1000 genomes]
rs9534880	0.91[ASN][1000 genomes]
rs9534882	0.90[ASN][1000 genomes]
rs9534885	0.91[ASN][1000 genomes]
rs9534889	0.88[ASN][1000 genomes]
rs9534892	0.86[ASN][1000 genomes]
rs9534896	0.85[ASN][1000 genomes]
rs9534897	0.83[ASN][1000 genomes]
rs9534898	0.86[ASN][1000 genomes]
rs9534901	0.86[ASN][1000 genomes]
rs9534903	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9534904	0.87[ASN][1000 genomes]
rs9534905	0.87[ASN][1000 genomes]
rs9534906	0.87[ASN][1000 genomes]
rs9534907	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9534908	0.87[ASN][1000 genomes]
rs9534909	0.85[ASN][1000 genomes]
rs9534912	0.87[ASN][1000 genomes]
rs9534913	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9534918	0.84[EUR][1000 genomes]
rs9534919	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9534922	0.84[ASN][1000 genomes]
rs9534923	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9534926	0.87[ASN][1000 genomes]
rs9534929	0.83[ASN][1000 genomes]
rs9562787	0.91[ASN][1000 genomes]
rs9567954	0.90[ASN][1000 genomes]
rs9567955	0.90[ASN][1000 genomes]
rs9567958	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9567959	0.91[ASN][1000 genomes]
rs9567960	0.91[ASN][1000 genomes]
rs9567963	0.91[ASN][1000 genomes]
rs9567964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9567972	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9567976	0.87[ASN][1000 genomes]
rs9567980	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9567986	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9595815	0.89[ASN][1000 genomes]
rs9595825	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4245347	SUCLA2	cis	Muscle Skeletal	GTEx
rs4245347	SUCLA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48507200-48548800	Weak transcription	Stomach Mucosa	stomach
2	chr13:48511000-48536600	Weak transcription	Esophagus	oesophagus
3	chr13:48512600-48537600	Weak transcription	Hela-S3	cervix
4	chr13:48514400-48574000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr13:48523000-48541600	Weak transcription	Psoas Muscle	Psoas
6	chr13:48523000-48542600	Weak transcription	K562	blood
7	chr13:48523200-48534000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr13:48523200-48536600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr13:48528000-48545800	Weak transcription	Colon Smooth Muscle	Colon
10	chr13:48528600-48541000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr13:48529200-48537200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr13:48529400-48537000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr13:48529400-48540200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
14	chr13:48529600-48535800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr13:48530000-48535200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
16	chr13:48530000-48537200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
17	chr13:48530000-48538400	ZNF genes & repeats	Dnd41	blood
18	chr13:48530000-48541000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:48530000-48541200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
20	chr13:48530400-48534200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
21	chr13:48530600-48534000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr13:48530600-48534200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr13:48530600-48534400	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr13:48530600-48537200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
25	chr13:48530600-48538400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
26	chr13:48530600-48538800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
27	chr13:48530600-48540200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr13:48530600-48540400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
29	chr13:48530800-48534200	ZNF genes & repeats	Fetal Kidney	kidney
30	chr13:48531000-48536800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr13:48531800-48534000	Weak transcription	Spleen	Spleen
32	chr13:48531800-48536600	Weak transcription	Pancreas	Pancrea
33	chr13:48532000-48536800	Weak transcription	Colonic Mucosa	Colon
34	chr13:48532000-48540800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr13:48532000-48551400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr13:48532200-48534000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr13:48532200-48534800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr13:48532200-48565200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr13:48532400-48534000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr13:48532400-48534000	Strong transcription	Primary B cells from cord blood	blood
41	chr13:48532400-48534000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr13:48532400-48534000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr13:48532400-48534000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr13:48532400-48534000	Weak transcription	Fetal Muscle Leg	muscle
45	chr13:48532400-48534000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr13:48532400-48536200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr13:48532400-48536400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr13:48532400-48536600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr13:48532400-48536600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr13:48532400-48536600	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links