Variant report

Variant	rs2053045
Chromosome Location	chr5:145612264-145612265
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:145607480..145610119-chr5:145611867..145613573,2	MCF-7	breast:

Extended variants
information (count: 159 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs10515565	0.89[ASN][1000 genomes]
rs10515566	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10515567	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1115080	0.81[ASN][1000 genomes]
rs11167937	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11540215	0.89[AMR][1000 genomes]
rs11948016	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11949351	0.89[AMR][1000 genomes]
rs11952445	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11953090	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11953506	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11954297	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11955206	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11955557	0.84[AMR][1000 genomes]
rs11957830	0.87[AMR][1000 genomes]
rs11957888	0.89[AMR][1000 genomes]
rs11957907	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11957998	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11958136	0.87[ASN][1000 genomes]
rs11958216	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11958633	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12152830	0.82[ASN][1000 genomes]
rs12153364	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12187277	0.90[ASN][1000 genomes]
rs12188772	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12189077	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13153891	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13154219	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13154735	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13155119	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13157279	0.89[AMR][1000 genomes]
rs13157784	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13159380	0.89[AMR][1000 genomes]
rs13160605	0.81[ASN][1000 genomes]
rs13160905	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13161036	0.89[AMR][1000 genomes]
rs13164872	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13168967	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13169370	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13169390	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13171596	0.89[AMR][1000 genomes]
rs13171939	0.89[ASN][1000 genomes]
rs13173347	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13173462	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13176784	0.86[AMR][1000 genomes]
rs13176915	0.89[AMR][1000 genomes]
rs13177015	0.84[ASN][1000 genomes]
rs13178443	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13178755	0.89[AMR][1000 genomes]
rs13179517	0.89[AMR][1000 genomes]
rs13180255	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13182948	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13183541	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13183976	0.88[ASN][1000 genomes]
rs13185586	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13186701	0.89[AMR][1000 genomes]
rs1368345	0.82[ASN][1000 genomes]
rs1506431	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1567057	0.87[ASN][1000 genomes]
rs17428647	0.89[AMR][1000 genomes]
rs17428724	0.89[AMR][1000 genomes]
rs17429180	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17443315	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17500927	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17501177	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17501601	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17502157	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17502233	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17502345	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17687490	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1864948	0.82[ASN][1000 genomes]
rs2014462	0.82[ASN][1000 genomes]
rs2014469	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2014473	0.82[ASN][1000 genomes]
rs2063002	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2279895	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2304032	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2304033	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2939523	0.84[ASN][1000 genomes]
rs2962515	0.85[AMR][1000 genomes]
rs2963926	0.87[ASN][1000 genomes]
rs33914983	0.89[AMR][1000 genomes]
rs34014355	0.89[AMR][1000 genomes]
rs34082425	0.90[ASN][1000 genomes]
rs34141601	0.89[ASN][1000 genomes]
rs34405762	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34444119	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34533649	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34775587	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34812645	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34819107	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34993855	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35048686	0.89[AMR][1000 genomes]
rs35142541	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35170264	0.84[ASN][1000 genomes]
rs35421100	0.89[AMR][1000 genomes]
rs35575652	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35870798	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35935643	0.89[ASN][1000 genomes]
rs35947468	0.87[ASN][1000 genomes]
rs36019024	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3937558	0.82[ASN][1000 genomes]
rs4413574	0.89[AMR][1000 genomes]
rs4443471	0.89[AMR][1000 genomes]
rs4705156	0.85[ASN][1000 genomes]
rs4705157	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4705179	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55665974	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55726586	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55799797	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55909935	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55937908	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56338615	0.89[AMR][1000 genomes]
rs56410805	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58848845	0.84[ASN][1000 genomes]
rs62372766	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62372767	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62372768	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62372769	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62372772	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62372773	0.87[ASN][1000 genomes]
rs62373809	0.82[AMR][1000 genomes]
rs62373810	0.82[AMR][1000 genomes]
rs62373811	0.85[AMR][1000 genomes]
rs62373812	0.89[AMR][1000 genomes]
rs62373813	0.89[AMR][1000 genomes]
rs62373819	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62373824	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62373831	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6580413	0.82[ASN][1000 genomes]
rs6867146	0.87[ASN][1000 genomes]
rs6868728	0.82[ASN][1000 genomes]
rs6878005	0.89[ASN][1000 genomes]
rs6881180	0.88[ASN][1000 genomes]
rs6882517	0.87[ASN][1000 genomes]
rs6884493	0.87[ASN][1000 genomes]
rs71594528	0.89[AMR][1000 genomes]
rs7443214	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7702123	0.85[ASN][1000 genomes]
rs7703269	0.85[ASN][1000 genomes]
rs7722258	0.87[ASN][1000 genomes]
rs7724811	0.87[ASN][1000 genomes]
rs7727353	0.84[ASN][1000 genomes]
rs7729098	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883006	chr5:145450586-145672431	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428128	chr5:145503978-145682880	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv883007	chr5:145506100-145672431	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv883008	chr5:145509728-145642925	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv883009	chr5:145567877-145672431	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv462475	chr5:145583623-145642007	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv599935	chr5:145583623-145642007	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv883010	chr5:145583623-145651979	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv883011	chr5:145583623-145672431	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
10	nsv523502	chr5:145588483-145639987	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv883012	chr5:145589542-145672431	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
12	nsv883013	chr5:145595837-145651979	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv462476	chr5:145604635-145622472	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv462477	chr5:145604635-145622472	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv599936	chr5:145604635-145622472	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2053045	LARS	cis	Thyroid	GTEx
rs2053045	LARS	Cis_1M	lymphoblastoid	RTeQTL
rs2053045	LARS	cis	Artery Tibial	GTEx
rs2053045	LARS	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:145584800-145631200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:145586400-145616800	Weak transcription	Right Ventricle	heart
3	chr5:145589000-145633200	Weak transcription	Brain Angular Gyrus	brain
4	chr5:145589200-145615400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:145593200-145615400	Weak transcription	Brain Substantia Nigra	brain
6	chr5:145593400-145651000	Weak transcription	Stomach Mucosa	stomach
7	chr5:145594600-145624200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr5:145596400-145616400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:145597000-145668400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:145597200-145616800	Weak transcription	NHDF-Ad	bronchial
11	chr5:145597200-145640600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:145597800-145617000	Weak transcription	HSMMtube	muscle
13	chr5:145598000-145627200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr5:145598000-145632200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr5:145598200-145623600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr5:145598200-145640400	Weak transcription	Psoas Muscle	Psoas
17	chr5:145598400-145629600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:145598400-145640400	Weak transcription	Fetal Heart	heart
19	chr5:145598600-145621800	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr5:145598800-145619800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr5:145598800-145620800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:145598800-145640600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:145599600-145619600	Weak transcription	Aorta	Aorta
24	chr5:145599800-145640200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr5:145601600-145623800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:145601800-145648200	Weak transcription	Fetal Brain Male	brain
27	chr5:145602200-145621000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr5:145602200-145625400	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr5:145602400-145619800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:145602600-145647000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:145602600-145653800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:145602800-145621800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:145602800-145622000	Strong transcription	Liver	Liver
34	chr5:145602800-145626800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr5:145603000-145621800	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr5:145603200-145612400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr5:145603600-145621400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr5:145604000-145620400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr5:145604000-145622400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:145605200-145614200	Strong transcription	Fetal Thymus	thymus
41	chr5:145606000-145621800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr5:145606000-145622600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr5:145606200-145614000	Strong transcription	Primary B cells from peripheral blood	blood
44	chr5:145606400-145612600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:145606400-145614000	Strong transcription	Primary B cells from cord blood	blood
46	chr5:145606400-145618000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:145606400-145619200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr5:145606400-145625600	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr5:145606600-145630000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr5:145607000-145615800	Weak transcription	Brain Inferior Temporal Lobe	brain

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