Variant report

Variant	rs61960454
Chromosome Location	chr13:50529608-50529609
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	chr13:50527779..50530040-chr13:50569450..50572377,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPRYD7-1	chr13:50526411-50531031	NONHSAT033771

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	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10492746	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1063181	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1063183	0.83[EUR][1000 genomes]
rs12100038	0.90[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	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12583637	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12583652	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12583823	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12584069	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12584122	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12585753	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12585966	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1323451	0.95[ASN][1000 genomes]
rs17073655	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17073682	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17073724	0.95[ASN][1000 genomes]
rs1807033	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2066540	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066546	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066547	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066552	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066553	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066555	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2066559	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2066562	0.95[AFR][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	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2181268	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2407881	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407882	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41308548	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4614628	0.83[EUR][1000 genomes]
rs55638467	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55727821	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55869555	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57230741	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59931782	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60574696	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60583460	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60828549	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60926548	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61960398	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61960442	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960445	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960446	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960447	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61960449	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960450	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960451	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960455	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960457	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961261	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961263	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961294	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961298	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961299	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961301	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961302	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961303	0.81[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	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561572	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[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	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7140070	0.86[AFR][1000 genomes]
rs7319351	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73194486	0.84[ASN][1000 genomes]
rs73196708	0.89[ASN][1000 genomes]
rs73196731	0.87[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	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7328892	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7334063	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7336477	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[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	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs790944	0.95[ASN][1000 genomes]
rs7982125	0.95[ASN][1000 genomes]
rs7984332	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[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	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990502	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7991454	0.83[EUR][1000 genomes]
rs7992903	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7994224	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7995557	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7997305	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997402	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997638	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7998223	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7998391	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9670083	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[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	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	esv1837591	chr13:50513148-50530603	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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
4	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
rs61960454	TRIM13	Cis_1M	lymphoblastoid	RTeQTL
rs61960454	DLEU1	Cis_1M	lymphoblastoid	RTeQTL
rs61960454	TRIM13	cis	Nerve Tibial	GTEx

Chromatin state (count:27 , 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	chr13:50525000-50530000	Enhancers	Placenta	Placenta
6	chr13:50525800-50532600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr13:50526200-50530000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr13:50528400-50530000	Enhancers	Fetal Intestine Large	intestine
9	chr13:50528600-50529800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr13:50528600-50530200	Enhancers	Fetal Intestine Small	intestine
11	chr13:50528600-50530400	Enhancers	Stomach Mucosa	stomach
12	chr13:50528800-50530000	Enhancers	HSMMtube	muscle
13	chr13:50529000-50529800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr13:50529000-50529800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr13:50529000-50529800	Enhancers	HepG2	liver
16	chr13:50529200-50529800	Enhancers	Duodenum Mucosa	Duodenum
17	chr13:50529200-50529800	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr13:50529200-50530400	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr13:50529400-50530600	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr13:50529400-50531000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr13:50529400-50531600	Weak transcription	Fetal Muscle Leg	muscle
22	chr13:50529400-50534000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr13:50529400-50547000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr13:50529600-50529800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr13:50529600-50531600	Weak transcription	Aorta	Aorta
26	chr13:50529600-50537000	Weak transcription	Psoas Muscle	Psoas
27	chr13:50529600-50550000	Weak transcription	Muscle Satellite Cultured Cells	--

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