Variant report

Variant	rs57230741
Chromosome Location	chr13:50559905-50559906
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50558774..50566292-chr13:50567433..50571184,7	K562	blood:
2	chr13:50558774..50562499-chr13:50568042..50570799,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPRYD7-1	chr13:50550469-50565502	NONHSAT033771
2	lnc-TRIM13-2	chr13:50559283-50560362	NONHSAT033779
3	lnc-SPRYD7-1	chr13:50559522-50560058	NONHSAT033780

Variant related genes	Relation type
ENSG00000264864	Chromatin interaction
ENSG00000204977	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1043208	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10492746	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1063181	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1063183	0.81[EUR][1000 genomes]
rs12100038	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12100048	0.95[ASN][1000 genomes]
rs12583615	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12583637	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12583652	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12583823	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12584069	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12584122	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12585753	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12585966	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1323451	0.95[ASN][1000 genomes]
rs17073655	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17073682	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17073724	0.95[ASN][1000 genomes]
rs1807033	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2066540	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066546	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066547	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066552	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066553	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066555	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2066559	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2066562	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2066565	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2066566	0.95[ASN][1000 genomes]
rs2177313	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2181267	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2181268	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2407881	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407882	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41308548	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4614628	0.81[EUR][1000 genomes]
rs55638467	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55727821	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55869555	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59931782	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60574696	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60583460	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60828549	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60926548	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61960398	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61960442	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960445	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960446	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960447	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61960449	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960450	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960451	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960454	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960455	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960457	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961261	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961263	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961294	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961298	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961299	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961301	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961302	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961303	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961304	0.95[ASN][1000 genomes]
rs61961305	0.95[ASN][1000 genomes]
rs61961306	0.95[AFR][1000 genomes]
rs61961323	0.95[ASN][1000 genomes]
rs61961324	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61961325	0.95[ASN][1000 genomes]
rs61961327	0.95[ASN][1000 genomes]
rs61961328	0.95[ASN][1000 genomes]
rs6561571	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561572	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561575	0.95[ASN][1000 genomes]
rs6561576	0.95[ASN][1000 genomes]
rs66559968	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs66756338	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7140070	0.86[AFR][1000 genomes]
rs7319351	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73194486	0.84[ASN][1000 genomes]
rs73196708	0.89[ASN][1000 genomes]
rs73196731	0.89[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	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7328892	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7334063	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7336477	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336927	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7339181	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs74078717	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs790944	0.95[ASN][1000 genomes]
rs7982125	0.95[ASN][1000 genomes]
rs7984332	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7984907	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7986364	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7986432	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990502	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7991454	0.81[EUR][1000 genomes]
rs7992903	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7994224	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7995557	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7997305	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997402	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997638	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7998223	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7998391	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9670083	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs57230741	TRIM13	Cis_1M	lymphoblastoid	RTeQTL
rs57230741	DLEU1	Cis_1M	lymphoblastoid	RTeQTL
rs57230741	TRIM13	cis	Nerve Tibial	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50539000-50570000	Weak transcription	Fetal Intestine Small	intestine
2	chr13:50540200-50562200	Weak transcription	Adipose Nuclei	Adipose
3	chr13:50540400-50569800	Weak transcription	Primary T cells from cord blood	blood
4	chr13:50543600-50570400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr13:50545800-50562000	Weak transcription	Fetal Intestine Large	intestine
6	chr13:50546000-50569200	Weak transcription	Primary B cells from cord blood	blood
7	chr13:50546000-50570000	Weak transcription	NHLF	lung
8	chr13:50547600-50561800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr13:50547600-50569800	Weak transcription	Dnd41	blood
10	chr13:50550800-50562200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr13:50550800-50569600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr13:50550800-50569800	Weak transcription	NH-A	brain
13	chr13:50551000-50560800	Weak transcription	Osteobl	bone
14	chr13:50551000-50562000	Weak transcription	HSMM	muscle
15	chr13:50551000-50562800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr13:50551000-50569600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr13:50551000-50569600	Weak transcription	Brain Hippocampus Middle	brain
18	chr13:50551000-50569800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr13:50551000-50569800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr13:50551000-50569800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr13:50551000-50570000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr13:50551000-50570200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr13:50551200-50562200	Weak transcription	NHDF-Ad	bronchial
24	chr13:50551200-50569600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr13:50551400-50570200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr13:50552400-50568800	Weak transcription	GM12878-XiMat	blood
27	chr13:50552400-50570200	Weak transcription	Lung	lung
28	chr13:50552800-50569800	Weak transcription	Fetal Lung	lung
29	chr13:50552800-50569800	Weak transcription	Placenta	Placenta
30	chr13:50552800-50570200	Weak transcription	Spleen	Spleen
31	chr13:50553600-50570000	Weak transcription	Left Ventricle	heart
32	chr13:50555000-50562800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr13:50555000-50569200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr13:50555200-50565800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr13:50555200-50569600	Weak transcription	Fetal Stomach	stomach
36	chr13:50555200-50569800	Weak transcription	Brain Angular Gyrus	brain
37	chr13:50556000-50568200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr13:50556800-50570200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr13:50557000-50569800	Weak transcription	Fetal Brain Female	brain
40	chr13:50557200-50570000	Weak transcription	Aorta	Aorta
41	chr13:50557600-50565200	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr13:50557600-50568600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr13:50558000-50560200	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr13:50558000-50566200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr13:50558000-50569600	Weak transcription	HUVEC	blood vessel
46	chr13:50558200-50570000	Weak transcription	Esophagus	oesophagus
47	chr13:50558600-50561800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr13:50558600-50566800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr13:50558600-50569800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr13:50558600-50569800	Weak transcription	HSMMtube	muscle

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