Variant report

Variant	rs62373823
Chromosome Location	chr5:145571995-145571996
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	chr5:145562850..145566563-chr5:145571128..145574037,3	MCF-7	breast:
2	chr5:145570785..145572816-chr5:145582211..145584363,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091009	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10515565	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1115080	0.82[EUR][1000 genomes]
rs11167936	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11540215	0.92[ASN][1000 genomes]
rs11948016	0.92[ASN][1000 genomes]
rs11949351	0.92[ASN][1000 genomes]
rs11950903	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11955557	0.90[ASN][1000 genomes]
rs11957830	0.92[ASN][1000 genomes]
rs11957888	0.92[ASN][1000 genomes]
rs11957998	0.92[ASN][1000 genomes]
rs11958136	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11958216	0.93[ASN][1000 genomes]
rs12152830	0.82[EUR][1000 genomes]
rs12187277	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12188772	0.92[ASN][1000 genomes]
rs13154735	0.92[ASN][1000 genomes]
rs13157279	0.92[ASN][1000 genomes]
rs13159380	0.92[ASN][1000 genomes]
rs13160605	0.82[EUR][1000 genomes]
rs13161036	0.92[ASN][1000 genomes]
rs13161488	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13162175	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13171596	0.92[ASN][1000 genomes]
rs13171939	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13175587	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13176784	0.92[ASN][1000 genomes]
rs13176915	0.92[ASN][1000 genomes]
rs13177015	0.80[EUR][1000 genomes]
rs13178755	0.92[ASN][1000 genomes]
rs13179296	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13179517	0.92[ASN][1000 genomes]
rs13183976	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13185518	0.82[EUR][1000 genomes]
rs13185586	0.92[ASN][1000 genomes]
rs13186701	0.92[ASN][1000 genomes]
rs1368345	0.82[EUR][1000 genomes]
rs1506431	0.89[ASN][1000 genomes]
rs1567057	0.85[EUR][1000 genomes]
rs17096590	0.82[EUR][1000 genomes]
rs17428647	0.92[ASN][1000 genomes]
rs17428724	0.92[ASN][1000 genomes]
rs17500927	0.92[ASN][1000 genomes]
rs1864948	0.82[EUR][1000 genomes]
rs1876189	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2014462	0.82[EUR][1000 genomes]
rs2014473	0.82[EUR][1000 genomes]
rs2063002	0.92[ASN][1000 genomes]
rs2279895	0.87[ASN][1000 genomes]
rs2895649	0.80[ASN][1000 genomes]
rs2939533	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2939535	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2962515	0.92[ASN][1000 genomes]
rs2963926	0.85[EUR][1000 genomes]
rs33914983	0.92[ASN][1000 genomes]
rs34014355	0.92[ASN][1000 genomes]
rs34082425	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34141601	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34405762	0.92[ASN][1000 genomes]
rs34519824	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34533649	0.89[ASN][1000 genomes]
rs35048686	0.92[ASN][1000 genomes]
rs35170264	0.80[EUR][1000 genomes]
rs35369194	0.82[EUR][1000 genomes]
rs35421100	0.92[ASN][1000 genomes]
rs35935643	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35947468	0.84[EUR][1000 genomes]
rs3937558	0.82[EUR][1000 genomes]
rs4413574	0.92[ASN][1000 genomes]
rs4443471	0.92[ASN][1000 genomes]
rs4705156	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4705445	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55665974	0.92[ASN][1000 genomes]
rs55799797	0.89[ASN][1000 genomes]
rs55909935	0.92[ASN][1000 genomes]
rs56240028	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56338615	0.92[ASN][1000 genomes]
rs56410805	0.92[ASN][1000 genomes]
rs56413906	0.82[EUR][1000 genomes]
rs58848845	0.82[EUR][1000 genomes]
rs62372773	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62373809	0.92[ASN][1000 genomes]
rs62373810	0.92[ASN][1000 genomes]
rs62373811	0.92[ASN][1000 genomes]
rs62373812	0.92[ASN][1000 genomes]
rs62373813	0.91[ASN][1000 genomes]
rs62373819	0.92[ASN][1000 genomes]
rs62373824	0.89[ASN][1000 genomes]
rs6580413	0.83[EUR][1000 genomes]
rs6861532	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6867146	0.82[EUR][1000 genomes]
rs6868728	0.82[EUR][1000 genomes]
rs6870878	0.82[EUR][1000 genomes]
rs6878005	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6881180	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6882517	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6884493	0.84[EUR][1000 genomes]
rs71594528	0.92[ASN][1000 genomes]
rs7443214	0.92[ASN][1000 genomes]
rs7702123	0.85[EUR][1000 genomes]
rs7703269	0.85[EUR][1000 genomes]
rs7711896	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7722258	0.85[EUR][1000 genomes]
rs7724811	0.84[EUR][1000 genomes]
rs7727353	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7729098	0.84[EUR][1000 genomes]
rs9918101	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9918130	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv3348501	chr5:145543808-145572250	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62373823	LARS	cis	Thyroid	GTEx
rs62373823	LARS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:145563000-145582200	Weak transcription	Right Atrium	heart
2	chr5:145570600-145572800	Weak transcription	NH-A	brain
3	chr5:145570800-145572200	Weak transcription	K562	blood
4	chr5:145570800-145572400	Weak transcription	HepG2	liver
5	chr5:145570800-145572800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:145570800-145573000	Weak transcription	Osteobl	bone
7	chr5:145571000-145572800	Weak transcription	NHEK	skin
8	chr5:145571000-145573000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:145571000-145582400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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