Variant report

Variant	rs55869555
Chromosome Location	chr13:50498787-50498788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1043208	0.84[ASN][1000 genomes]
rs10492746	0.84[ASN][1000 genomes]
rs1063181	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1063183	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12100038	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12100048	0.84[ASN][1000 genomes]
rs12583615	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12583637	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12583652	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12583823	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12584069	0.84[ASN][1000 genomes]
rs12584122	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12585753	0.84[ASN][1000 genomes]
rs12585966	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1323451	0.84[ASN][1000 genomes]
rs17073655	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17073682	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17073724	0.84[ASN][1000 genomes]
rs1807033	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066540	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2066546	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2066547	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2066552	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2066553	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2066555	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2066559	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2066562	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2066565	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2066566	0.84[ASN][1000 genomes]
rs2177313	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2181267	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181268	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407881	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2407882	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41308548	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4614628	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55638467	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55727821	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57230741	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59086590	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs59931782	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60574696	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60583460	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60828549	0.87[AFR][1000 genomes]
rs60926548	0.84[ASN][1000 genomes]
rs61960398	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61960442	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960445	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960446	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960447	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61960449	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960450	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960451	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960454	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960455	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960457	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61961261	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61961263	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61961294	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61961298	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61961299	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61961301	0.84[ASN][1000 genomes]
rs61961302	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61961303	0.84[ASN][1000 genomes]
rs61961304	0.84[ASN][1000 genomes]
rs61961305	0.84[ASN][1000 genomes]
rs61961306	0.87[AFR][1000 genomes]
rs61961323	0.84[ASN][1000 genomes]
rs61961324	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs61961325	0.84[ASN][1000 genomes]
rs61961327	0.84[ASN][1000 genomes]
rs61961328	0.84[ASN][1000 genomes]
rs6561571	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6561572	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6561575	0.84[ASN][1000 genomes]
rs6561576	0.84[ASN][1000 genomes]
rs66559968	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs66756338	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7140070	0.81[AFR][1000 genomes]
rs7319351	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73194486	0.95[ASN][1000 genomes]
rs73196708	1.00[ASN][1000 genomes]
rs73196731	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73196734	0.84[ASN][1000 genomes]
rs732729	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7328892	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334063	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7336477	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7336927	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7339181	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs74078717	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs790944	0.84[ASN][1000 genomes]
rs7982125	0.84[ASN][1000 genomes]
rs7984332	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7984907	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7986364	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7986432	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7990502	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7991454	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7992903	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7994224	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7995557	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997305	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7997402	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7997638	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7998223	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7998391	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9670083	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1851738	chr13:50474326-50507944	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs55869555	TRIM13	cis	Nerve Tibial	GTEx
rs55869555	TRIM13	Cis_1M	lymphoblastoid	RTeQTL
rs55869555	DLEU1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50477800-50499600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr13:50479600-50508600	Weak transcription	K562	blood
3	chr13:50479800-50500000	Weak transcription	Colon Smooth Muscle	Colon
4	chr13:50480800-50508800	Weak transcription	Fetal Brain Male	brain
5	chr13:50481800-50509600	Weak transcription	Right Ventricle	heart
6	chr13:50482600-50509600	Weak transcription	Primary B cells from cord blood	blood
7	chr13:50484000-50509600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:50484400-50501800	Weak transcription	HSMMtube	muscle
9	chr13:50484400-50509400	Weak transcription	Fetal Kidney	kidney
10	chr13:50484600-50509600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr13:50485000-50499400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr13:50485800-50501800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr13:50485800-50506200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr13:50485800-50509200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr13:50486000-50503400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr13:50486000-50503400	Strong transcription	Liver	Liver
17	chr13:50486000-50509400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr13:50486400-50509600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr13:50486600-50508800	Weak transcription	Hela-S3	cervix
20	chr13:50487400-50509400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr13:50487600-50509400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr13:50488000-50500400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr13:50488400-50509600	Weak transcription	Colonic Mucosa	Colon
24	chr13:50489200-50509600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr13:50489200-50510000	Weak transcription	Spleen	Spleen
26	chr13:50489600-50501000	Strong transcription	Osteobl	bone
27	chr13:50489600-50502400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr13:50489600-50503200	Strong transcription	Adipose Nuclei	Adipose
29	chr13:50489600-50504200	Strong transcription	Fetal Intestine Large	intestine
30	chr13:50490000-50499400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr13:50490000-50501400	Weak transcription	Fetal Thymus	thymus
32	chr13:50490200-50502800	Strong transcription	Duodenum Mucosa	Duodenum
33	chr13:50490200-50503000	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr13:50490600-50499600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr13:50490800-50502000	Weak transcription	Primary T cells from cord blood	blood
36	chr13:50490800-50506200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr13:50491200-50507000	Weak transcription	Brain Angular Gyrus	brain
38	chr13:50491800-50501200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr13:50492200-50504600	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr13:50492200-50509400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr13:50492400-50509600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr13:50492600-50508800	Weak transcription	HUVEC	blood vessel
43	chr13:50492800-50509400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr13:50492800-50509600	Weak transcription	Aorta	Aorta
45	chr13:50493400-50502000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr13:50493400-50509400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr13:50493600-50500000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr13:50493800-50509600	Weak transcription	Lung	lung
49	chr13:50494000-50502800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr13:50494200-50508800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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