Variant report

Variant	rs61960457
Chromosome Location	chr13:50530914-50530915
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPRYD7-1	chr13:50526411-50531031	NONHSAT033771
2	lnc-SPRYD7-1	chr13:50530843-50531031	NONHSAT033774
3	lnc-SPRYD7-1	chr13:50530843-50531031	NONHSAT140129

Extended variants
information (count: 110 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1043208	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10492746	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1063181	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1063183	0.92[EUR][1000 genomes]
rs12100038	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12100048	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12583615	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12583637	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12583652	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12583823	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12584069	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12584122	0.83[EUR][1000 genomes]
rs12585753	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12585966	0.81[EUR][1000 genomes]
rs1323451	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17073655	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17073682	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17073724	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1807033	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2066540	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066546	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066547	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066552	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066553	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066555	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2066559	0.95[ASN][1000 genomes]
rs2066562	0.95[ASN][1000 genomes]
rs2066565	0.95[ASN][1000 genomes]
rs2066566	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2177313	0.95[ASN][1000 genomes]
rs2181267	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2181268	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2407881	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407882	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41308548	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4614628	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55638467	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55727821	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55869555	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57230741	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59931782	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60574696	0.83[EUR][1000 genomes]
rs60583460	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60828549	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60926548	0.95[ASN][1000 genomes]
rs61960398	0.83[EUR][1000 genomes]
rs61960442	0.89[ASN][1000 genomes]
rs61960445	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960446	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960447	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61960449	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960450	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960451	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960454	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960455	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961261	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961263	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961294	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961298	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961299	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961301	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961302	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961303	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961304	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61961305	0.95[ASN][1000 genomes]
rs61961323	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61961324	0.95[ASN][1000 genomes]
rs61961325	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61961327	0.95[ASN][1000 genomes]
rs61961328	0.95[ASN][1000 genomes]
rs6561571	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561572	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561575	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6561576	0.95[ASN][1000 genomes]
rs66559968	0.95[ASN][1000 genomes]
rs66756338	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7319351	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73194486	0.84[ASN][1000 genomes]
rs73196708	0.89[ASN][1000 genomes]
rs73196731	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73196734	0.95[ASN][1000 genomes]
rs73196744	0.89[ASN][1000 genomes]
rs7325993	0.81[ASN][1000 genomes]
rs732729	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7328892	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7334063	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7336477	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336927	0.95[ASN][1000 genomes]
rs7339181	0.95[ASN][1000 genomes]
rs74078717	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs790944	0.95[ASN][1000 genomes]
rs7982125	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7984332	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7984907	0.95[ASN][1000 genomes]
rs7986364	0.95[ASN][1000 genomes]
rs7986432	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990502	0.87[EUR][1000 genomes]
rs7991454	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7992903	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7994224	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7995557	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7997305	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997638	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7998223	0.95[ASN][1000 genomes]
rs7998391	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9670083	0.83[EUR][1000 genomes];0.89[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	esv1834429	chr13:50509784-50536186	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
3	nsv561630	chr13:50525141-50545402	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs61960457	TRIM13	Cis_1M	lymphoblastoid	RTeQTL
rs61960457	TRIM13	cis	Nerve Tibial	GTEx
rs61960457	DLEU1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50511400-50537800	Weak transcription	Left Ventricle	heart
2	chr13:50513400-50532600	Weak transcription	Ovary	ovary
3	chr13:50513400-50532800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr13:50522400-50550600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr13:50525800-50532600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr13:50529400-50531000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr13:50529400-50531600	Weak transcription	Fetal Muscle Leg	muscle
8	chr13:50529400-50534000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr13:50529400-50547000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr13:50529600-50531600	Weak transcription	Aorta	Aorta
11	chr13:50529600-50537000	Weak transcription	Psoas Muscle	Psoas
12	chr13:50529600-50550000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr13:50529800-50532600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr13:50529800-50536600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr13:50529800-50539400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr13:50529800-50543200	Weak transcription	Osteobl	bone
17	chr13:50529800-50544800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr13:50530000-50536400	Weak transcription	Placenta	Placenta
19	chr13:50530000-50546600	Weak transcription	Fetal Thymus	thymus
20	chr13:50530400-50537200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr13:50530600-50533000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr13:50530800-50533200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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