Variant report

Variant	rs4942730
Chromosome Location	chr13:48553052-48553053
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 142 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs1041070	0.83[ASN][1000 genomes]
rs11148099	0.85[ASN][1000 genomes]
rs11148100	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11618397	0.81[ASN][1000 genomes]
rs1185727	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12864691	0.88[AFR][1000 genomes]
rs1326135	0.83[ASN][1000 genomes]
rs1326136	0.81[ASN][1000 genomes]
rs1536301	0.81[ASN][1000 genomes]
rs1544078	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1886975	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1886976	0.82[ASN][1000 genomes]
rs1926089	0.81[ASN][1000 genomes]
rs2031590	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2031591	0.86[AFR][1000 genomes]
rs2094194	0.82[ASN][1000 genomes]
rs2148243	0.84[ASN][1000 genomes]
rs2148244	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2148245	0.81[ASN][1000 genomes]
rs2182376	0.83[ASN][1000 genomes]
rs2296573	0.87[AFR][1000 genomes]
rs2296574	0.83[ASN][1000 genomes]
rs2406693	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2406697	0.83[ASN][1000 genomes]
rs2406699	0.80[ASN][1000 genomes]
rs4245347	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4447314	0.83[ASN][1000 genomes]
rs4522322	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4941621	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4942726	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4942727	0.80[ASN][1000 genomes]
rs4942728	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4942729	0.84[ASN][1000 genomes]
rs4942735	0.83[ASN][1000 genomes]
rs4942739	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs61973260	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6561417	0.81[ASN][1000 genomes]
rs6561419	0.84[ASN][1000 genomes]
rs6561420	0.84[ASN][1000 genomes]
rs6561424	0.83[ASN][1000 genomes]
rs6561427	0.83[ASN][1000 genomes]
rs6561430	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6561431	0.82[ASN][1000 genomes]
rs6561432	0.82[ASN][1000 genomes]
rs718010	0.81[ASN][1000 genomes]
rs7318770	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7319245	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7320366	0.83[ASN][1000 genomes]
rs7320461	0.81[ASN][1000 genomes]
rs7320759	0.81[ASN][1000 genomes]
rs7322515	0.84[ASN][1000 genomes]
rs7325189	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7325437	0.82[ASN][1000 genomes]
rs7326889	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7326984	0.84[ASN][1000 genomes]
rs7327260	0.81[ASN][1000 genomes]
rs7327730	0.83[ASN][1000 genomes]
rs7328525	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7328537	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7329419	0.85[ASN][1000 genomes]
rs7330130	0.82[ASN][1000 genomes]
rs7331285	0.82[ASN][1000 genomes]
rs7332304	0.82[ASN][1000 genomes]
rs7333659	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7333821	0.81[ASN][1000 genomes]
rs7334207	0.81[ASN][1000 genomes]
rs7335788	0.81[ASN][1000 genomes]
rs7336972	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7337004	0.82[ASN][1000 genomes]
rs7337744	0.83[ASN][1000 genomes]
rs7338125	0.81[ASN][1000 genomes]
rs7338373	0.82[ASN][1000 genomes]
rs765809	0.81[ASN][1000 genomes]
rs7989231	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7990244	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7990266	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7990505	0.84[ASN][1000 genomes]
rs7994359	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7996580	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7997802	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7998116	0.83[ASN][1000 genomes]
rs7998260	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7998497	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7998998	0.83[ASN][1000 genomes]
rs8000164	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8001432	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8001871	0.90[AFR][1000 genomes]
rs9316339	0.83[ASN][1000 genomes]
rs9316343	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9316344	0.83[ASN][1000 genomes]
rs9526422	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9526423	0.81[ASN][1000 genomes]
rs9526424	0.82[ASN][1000 genomes]
rs9526426	0.81[ASN][1000 genomes]
rs9526429	0.83[ASN][1000 genomes]
rs9526430	0.83[ASN][1000 genomes]
rs9526433	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9526434	0.82[ASN][1000 genomes]
rs9534876	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9534877	0.81[ASN][1000 genomes]
rs9534878	0.81[ASN][1000 genomes]
rs9534879	0.81[ASN][1000 genomes]
rs9534880	0.81[ASN][1000 genomes]
rs9534882	0.80[ASN][1000 genomes]
rs9534885	0.81[ASN][1000 genomes]
rs9534889	0.84[ASN][1000 genomes]
rs9534892	0.83[ASN][1000 genomes]
rs9534896	0.82[ASN][1000 genomes]
rs9534897	0.80[ASN][1000 genomes]
rs9534898	0.83[ASN][1000 genomes]
rs9534901	0.83[ASN][1000 genomes]
rs9534903	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9534904	0.83[ASN][1000 genomes]
rs9534905	0.83[ASN][1000 genomes]
rs9534906	0.83[ASN][1000 genomes]
rs9534907	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9534908	0.83[ASN][1000 genomes]
rs9534909	0.82[ASN][1000 genomes]
rs9534912	0.83[ASN][1000 genomes]
rs9534913	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9534918	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9534919	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9534922	0.80[ASN][1000 genomes]
rs9534923	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9534926	0.83[ASN][1000 genomes]
rs9534929	0.80[ASN][1000 genomes]
rs9562787	0.81[ASN][1000 genomes]
rs9567954	0.83[ASN][1000 genomes]
rs9567955	0.83[ASN][1000 genomes]
rs9567958	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9567959	0.81[ASN][1000 genomes]
rs9567960	0.81[ASN][1000 genomes]
rs9567963	0.81[ASN][1000 genomes]
rs9567964	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9567972	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9567976	0.83[ASN][1000 genomes]
rs9567980	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9567986	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9595815	0.82[ASN][1000 genomes]
rs9595825	0.81[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
rs4942730	SUCLA2	cis	Muscle Skeletal	GTEx
rs4942730	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	chr13:48514400-48574000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr13:48532200-48565200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr13:48532400-48559400	Weak transcription	Gastric	stomach
4	chr13:48532400-48565200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr13:48534000-48560800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr13:48534200-48573200	Weak transcription	Brain Angular Gyrus	brain
7	chr13:48534400-48574400	Weak transcription	Small Intestine	intestine
8	chr13:48535000-48564800	Weak transcription	NHLF	lung
9	chr13:48537200-48574200	Weak transcription	Colonic Mucosa	Colon
10	chr13:48537400-48560200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr13:48537400-48574000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr13:48537400-48574400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr13:48538000-48567200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr13:48538400-48574000	Weak transcription	Hela-S3	cervix
15	chr13:48538600-48559800	Weak transcription	HUVEC	blood vessel
16	chr13:48538800-48564800	Weak transcription	Brain Germinal Matrix	brain
17	chr13:48539600-48571200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr13:48540000-48574200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr13:48540200-48559000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr13:48540800-48565000	Weak transcription	NH-A	brain
21	chr13:48542000-48558800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr13:48542400-48564800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr13:48542400-48565200	Weak transcription	Psoas Muscle	Psoas
24	chr13:48542400-48567000	Weak transcription	Esophagus	oesophagus
25	chr13:48542800-48553800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr13:48542800-48559000	Weak transcription	HSMM	muscle
27	chr13:48543000-48553600	Weak transcription	Fetal Kidney	kidney
28	chr13:48543000-48574400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr13:48543400-48560600	Weak transcription	HepG2	liver
30	chr13:48546400-48559400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr13:48546400-48564600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr13:48546400-48565200	Weak transcription	Pancreas	Pancrea
33	chr13:48546600-48559200	Weak transcription	Brain Substantia Nigra	brain
34	chr13:48546600-48574400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr13:48546600-48574800	Weak transcription	Spleen	Spleen
36	chr13:48546800-48559000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr13:48546800-48559000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr13:48546800-48559200	Weak transcription	Colon Smooth Muscle	Colon
39	chr13:48546800-48560600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr13:48546800-48564200	Weak transcription	Lung	lung
41	chr13:48546800-48564600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr13:48546800-48567000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr13:48546800-48567200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr13:48546800-48571600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr13:48547000-48559200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr13:48547400-48559200	Weak transcription	Brain Anterior Caudate	brain
47	chr13:48547800-48559200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr13:48548000-48557400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr13:48548000-48559000	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr13:48548000-48559000	Weak transcription	Primary T cells fromperipheralblood	blood

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