Variant report

Variant	rs2024056
Chromosome Location	chr5:145466278-145466279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:145425852..145428406-chr5:145465535..145467053,2	K562	blood:
2	chr5:145464130..145467006-chr5:145471609..145474938,3	K562	blood:
3	chr5:145465495..145467828-chr5:145478928..145481354,2	K562	blood:
4	chr5:145456217..145460713-chr5:145463398..145466718,4	K562	blood:

Variant related genes	Relation type
ENSG00000251556	Chromatin interaction

Extended variants
information (count: 174 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:173)

rs_ID	r²[population]
rs1006204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10491259	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10491260	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10491261	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10515564	1.00[JPT][hapmap]
rs10515565	0.85[CEU][hapmap]
rs10515567	0.80[JPT][hapmap]
rs1054020	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11167932	1.00[JPT][hapmap]
rs11167936	0.81[EUR][1000 genomes]
rs11948314	1.00[JPT][hapmap]
rs11949352	0.82[ASN][1000 genomes]
rs11950903	0.81[EUR][1000 genomes]
rs11952697	0.81[ASN][1000 genomes]
rs11953517	1.00[JPT][hapmap]
rs11953586	0.99[ASN][1000 genomes]
rs11954750	1.00[JPT][hapmap]
rs11954977	1.00[JPT][hapmap]
rs11955443	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11956508	1.00[ASN][1000 genomes]
rs11957998	0.94[JPT][hapmap]
rs11958136	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs11960510	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12153109	1.00[JPT][hapmap]
rs12186358	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12186642	0.81[ASN][1000 genomes]
rs12187128	0.81[ASN][1000 genomes]
rs12187277	0.85[CEU][hapmap];0.80[JPT][hapmap]
rs12187649	0.81[ASN][1000 genomes]
rs12187913	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12188066	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12188581	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12189385	1.00[JPT][hapmap]
rs12374457	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12374516	0.90[ASN][1000 genomes]
rs12374538	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12374539	0.82[ASN][1000 genomes]
rs13153675	1.00[JPT][hapmap]
rs13161075	1.00[JPT][hapmap]
rs13161488	0.81[EUR][1000 genomes]
rs13161659	1.00[JPT][hapmap]
rs13162175	0.81[EUR][1000 genomes]
rs13171939	0.84[CEU][hapmap];0.80[JPT][hapmap]
rs13173462	0.84[JPT][hapmap]
rs13175587	0.81[EUR][1000 genomes]
rs13175806	0.82[ASN][1000 genomes]
rs13178370	1.00[JPT][hapmap]
rs13178516	1.00[JPT][hapmap]
rs13178840	1.00[JPT][hapmap]
rs13179296	0.81[EUR][1000 genomes]
rs13180255	0.80[JPT][hapmap]
rs13181074	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13181077	0.89[ASN][1000 genomes]
rs13182302	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13182567	1.00[JPT][hapmap]
rs13183976	0.84[CEU][hapmap];0.80[JPT][hapmap]
rs13186694	1.00[JPT][hapmap]
rs1395277	1.00[JPT][hapmap]
rs1567057	0.84[CEU][hapmap];0.80[JPT][hapmap]
rs17104255	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17212373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17212380	0.99[ASN][1000 genomes]
rs17427286	1.00[JPT][hapmap]
rs17427691	1.00[JPT][hapmap]
rs17428100	1.00[JPT][hapmap]
rs17428465	1.00[JPT][hapmap]
rs17428570	1.00[JPT][hapmap]
rs17428724	1.00[JPT][hapmap]
rs17492851	1.00[JPT][hapmap]
rs17492893	1.00[JPT][hapmap]
rs17492950	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17493090	1.00[JPT][hapmap]
rs17500483	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17500504	1.00[JPT][hapmap]
rs17501177	0.80[JPT][hapmap]
rs17796852	0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs17796858	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17796864	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17796870	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17796876	1.00[ASN][1000 genomes]
rs1876189	0.81[EUR][1000 genomes]
rs1911112	1.00[JPT][hapmap]
rs1911113	1.00[JPT][hapmap]
rs1985600	1.00[ASN][1000 genomes]
rs2024055	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2024057	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2063002	1.00[JPT][hapmap]
rs2063005	0.96[CEU][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2116749	0.85[CEU][hapmap];0.80[JPT][hapmap]
rs2240524	0.98[ASN][1000 genomes]
rs2279895	1.00[JPT][hapmap]
rs2302036	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2304032	0.80[JPT][hapmap]
rs2304033	0.84[JPT][hapmap]
rs2400209	1.00[JPT][hapmap]
rs2400211	1.00[JPT][hapmap]
rs2895647	1.00[JPT][hapmap]
rs2895648	1.00[JPT][hapmap]
rs2895649	1.00[JPT][hapmap]
rs2939533	0.82[EUR][1000 genomes]
rs2939535	0.89[EUR][1000 genomes]
rs2939536	1.00[JPT][hapmap]
rs2939539	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2962502	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2962503	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2962509	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2962510	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2962511	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2963914	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2963915	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2963918	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2963919	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2963920	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2963921	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2963922	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2963923	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34071526	1.00[ASN][1000 genomes]
rs34078408	1.00[ASN][1000 genomes]
rs34160255	0.82[ASN][1000 genomes]
rs34170515	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs34516108	0.82[ASN][1000 genomes]
rs34530601	1.00[ASN][1000 genomes]
rs34601905	0.81[ASN][1000 genomes]
rs34818573	1.00[ASN][1000 genomes]
rs34818690	1.00[ASN][1000 genomes]
rs34848484	0.90[ASN][1000 genomes]
rs35048100	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35150639	1.00[ASN][1000 genomes]
rs35228139	1.00[ASN][1000 genomes]
rs35283996	0.87[ASN][1000 genomes]
rs35291206	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35652702	0.81[ASN][1000 genomes]
rs35801832	0.81[ASN][1000 genomes]
rs35917756	0.99[ASN][1000 genomes]
rs3749994	1.00[JPT][hapmap]
rs3763373	0.89[JPT][hapmap]
rs3797626	0.99[ASN][1000 genomes]
rs3797627	0.99[ASN][1000 genomes]
rs3797628	1.00[JPT][hapmap]
rs3822623	0.94[JPT][hapmap]
rs3828935	0.94[JPT][hapmap]
rs41338847	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4413574	1.00[JPT][hapmap]
rs4705156	0.89[CEU][hapmap];0.80[JPT][hapmap]
rs4705179	0.80[JPT][hapmap]
rs4705445	0.81[EUR][1000 genomes]
rs4913061	0.90[ASN][1000 genomes]
rs4913062	1.00[ASN][1000 genomes]
rs4913064	1.00[JPT][hapmap]
rs4913065	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4913066	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55782203	0.81[ASN][1000 genomes]
rs55874924	0.99[ASN][1000 genomes]
rs56240028	0.81[EUR][1000 genomes]
rs56338521	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56393319	0.90[ASN][1000 genomes]
rs6580408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67829086	0.82[ASN][1000 genomes]
rs68022863	0.86[ASN][1000 genomes]
rs6862371	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6877277	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6878005	0.84[CEU][hapmap]
rs6881180	0.81[CEU][hapmap];0.80[JPT][hapmap]
rs6892928	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7443214	1.00[JPT][hapmap]
rs7711896	0.81[EUR][1000 genomes]
rs7722258	0.85[CEU][hapmap];0.80[JPT][hapmap]
rs7725078	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7728381	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7728631	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7729098	0.84[CEU][hapmap];0.80[JPT][hapmap]
rs9918101	0.92[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes]
rs9918130	0.87[CEU][hapmap];0.96[YRI][hapmap];0.81[EUR][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2024056	LARS	Cis_1M	lymphoblastoid	RTeQTL
rs2024056	LARS	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:145459800-145471200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:145459800-145492000	Weak transcription	HSMMtube	muscle

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