Variant report

Variant	rs2066547
Chromosome Location	chr13:50580089-50580090
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50569577..50572074-chr13:50579319..50584996,5	MCF-7	breast:
2	chr13:50572788..50574418-chr13:50579406..50581918,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204977	Chromatin interaction
ENSG00000264864	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1043208	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10492746	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1063181	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1063183	0.81[EUR][1000 genomes]
rs12100038	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12100048	1.00[ASN][1000 genomes]
rs12583615	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583637	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583652	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583823	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12584069	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12584122	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12585753	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12585966	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1323451	1.00[ASN][1000 genomes]
rs17073655	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17073682	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17073724	1.00[ASN][1000 genomes]
rs1807033	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2066540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066552	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066553	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066555	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2066559	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2066562	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2066565	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2066566	1.00[ASN][1000 genomes]
rs2177313	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2181267	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2181268	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2407881	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2407882	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41308548	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4614628	0.81[EUR][1000 genomes]
rs55638467	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55727821	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55869555	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57230741	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59931782	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60574696	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs60583460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60828549	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60926548	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61960398	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61960442	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61960445	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61960446	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61960447	0.83[EUR][1000 genomes]
rs61960449	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61960450	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61960451	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61960454	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61960455	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61960457	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961261	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961263	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961294	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961298	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961299	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961301	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961302	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961303	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961304	1.00[ASN][1000 genomes]
rs61961305	1.00[ASN][1000 genomes]
rs61961306	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61961323	1.00[ASN][1000 genomes]
rs61961324	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61961325	1.00[ASN][1000 genomes]
rs61961327	1.00[ASN][1000 genomes]
rs61961328	1.00[ASN][1000 genomes]
rs6561571	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6561572	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6561575	1.00[ASN][1000 genomes]
rs6561576	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66559968	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66756338	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140070	0.87[AFR][1000 genomes]
rs7319351	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73196708	0.84[ASN][1000 genomes]
rs73196731	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73196734	1.00[ASN][1000 genomes]
rs73196744	0.95[ASN][1000 genomes]
rs7325993	0.86[ASN][1000 genomes]
rs732729	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7328892	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7334063	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336477	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7336927	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7339181	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74078717	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs790944	1.00[ASN][1000 genomes]
rs7982125	1.00[ASN][1000 genomes]
rs7984332	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7984907	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7986364	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7986432	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7990502	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7991454	0.81[EUR][1000 genomes]
rs7992903	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7994224	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7995557	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7997305	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7997402	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7997638	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998223	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7998391	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9670083	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[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
rs2066547	TRIM13	cis	Nerve Tibial	GTEx
rs2066547	DLEU1	Cis_1M	lymphoblastoid	RTeQTL
rs2066547	TRIM13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50571800-50585200	Weak transcription	Gastric	stomach
2	chr13:50572000-50585800	Weak transcription	Ovary	ovary
3	chr13:50572600-50589600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:50572800-50584400	Weak transcription	K562	blood
5	chr13:50573000-50594600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:50573400-50580400	Weak transcription	Small Intestine	intestine
7	chr13:50573800-50581000	Strong transcription	Fetal Thymus	thymus
8	chr13:50573800-50585000	Weak transcription	Left Ventricle	heart
9	chr13:50573800-50585800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr13:50573800-50588600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr13:50573800-50589400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr13:50573800-50590200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr13:50574000-50580400	Strong transcription	Osteobl	bone
14	chr13:50574000-50584800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr13:50574000-50585000	Weak transcription	Aorta	Aorta
16	chr13:50574000-50585600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr13:50574000-50586000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr13:50574000-50599600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr13:50574200-50581200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr13:50574200-50589000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr13:50574200-50591000	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr13:50574600-50588800	Weak transcription	Stomach Mucosa	stomach
23	chr13:50574800-50580400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr13:50574800-50580400	Weak transcription	Brain Substantia Nigra	brain
25	chr13:50574800-50580600	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr13:50574800-50580800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr13:50574800-50580800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr13:50574800-50584400	Weak transcription	Fetal Heart	heart
29	chr13:50574800-50584600	Weak transcription	Adipose Nuclei	Adipose
30	chr13:50574800-50584600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr13:50574800-50584600	Weak transcription	HMEC	breast
32	chr13:50574800-50585000	Weak transcription	NHEK	skin
33	chr13:50574800-50585800	Weak transcription	Fetal Kidney	kidney
34	chr13:50574800-50586200	Weak transcription	HepG2	liver
35	chr13:50574800-50588000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr13:50574800-50588600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr13:50575000-50580400	Weak transcription	NHLF	lung
38	chr13:50575000-50586200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr13:50575200-50580400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr13:50575200-50581200	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr13:50575200-50583400	Weak transcription	HUVEC	blood vessel
42	chr13:50575600-50588600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr13:50575800-50580200	Weak transcription	A549	lung
44	chr13:50575800-50580400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr13:50575800-50581400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr13:50575800-50586400	Weak transcription	Hela-S3	cervix
47	chr13:50576000-50580400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr13:50576200-50584600	Strong transcription	Fetal Intestine Small	intestine
49	chr13:50576400-50580800	Strong transcription	Fetal Intestine Large	intestine
50	chr13:50576400-50586400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links