Variant report

Variant	rs564252
Chromosome Location	chr1:59018894-59018895
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	chr1:59010376..59013266-chr1:59015138..59019159,5	K562	blood:
2	chr1:59010739..59013825-chr1:59014370..59019048,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OMA1-1	chr1:59018585-59019005	NONHSAT003506

Variant related genes	Relation type
ENSG00000162600	Chromatin interaction
ENSG00000173406	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10218842	0.88[EUR][1000 genomes]
rs10489816	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs11207256	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11207257	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11799408	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs11799415	0.88[EUR][1000 genomes]
rs11799786	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11800241	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11801938	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs11802520	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs11803703	0.80[EUR][1000 genomes]
rs11805031	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs11807046	0.88[EUR][1000 genomes]
rs11808437	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11808438	0.82[EUR][1000 genomes]
rs11808738	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs11809508	0.86[CEU][hapmap]
rs11809967	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12024500	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1503646	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1503647	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1503648	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1627332	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17117574	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17117627	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17117643	0.86[CEU][hapmap]
rs17117647	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17117678	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17447078	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17498811	0.91[CEU][hapmap]
rs17506467	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1775001	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs179798	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs1847350	0.85[EUR][1000 genomes]
rs1847351	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1891435	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs232843	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs232845	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs232846	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2406783	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs338234	1.00[CEU][hapmap]
rs35075952	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41296155	0.90[EUR][1000 genomes]
rs41311174	0.99[EUR][1000 genomes]
rs488606	1.00[CEU][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4912196	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs4912341	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4912342	0.88[EUR][1000 genomes]
rs4912343	0.88[EUR][1000 genomes]
rs4912345	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs4912346	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs4912347	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs492988	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs511687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs512462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs518070	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs530095	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs532134	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs542727	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs544596	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs546271	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs546358	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs548275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55712302	0.88[EUR][1000 genomes]
rs55721304	0.90[EUR][1000 genomes]
rs56109164	0.96[EUR][1000 genomes]
rs565008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs565617	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs565954	1.00[CEU][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs567787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs573135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs586847	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs593279	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs594973	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs595909	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61779267	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61779289	0.99[EUR][1000 genomes]
rs61779290	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61779294	0.92[EUR][1000 genomes]
rs61781782	0.80[EUR][1000 genomes]
rs61781784	0.80[EUR][1000 genomes]
rs61781785	0.80[EUR][1000 genomes]
rs61781787	0.80[EUR][1000 genomes]
rs61781789	0.80[EUR][1000 genomes]
rs61781790	0.80[EUR][1000 genomes]
rs61781792	0.88[EUR][1000 genomes]
rs61781813	0.88[EUR][1000 genomes]
rs61781816	0.88[EUR][1000 genomes]
rs61781818	0.88[EUR][1000 genomes]
rs61781819	0.84[EUR][1000 genomes]
rs61781821	0.82[EUR][1000 genomes]
rs61781822	0.82[EUR][1000 genomes]
rs61781823	0.82[EUR][1000 genomes]
rs61781824	0.82[EUR][1000 genomes]
rs621754	1.00[CEU][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs627633	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs628623	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs635775	1.00[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs641929	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs644928	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs654299	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs657202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs657711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6587829	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs664570	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6662028	0.80[EUR][1000 genomes]
rs6662905	0.87[EUR][1000 genomes]
rs6663128	0.82[EUR][1000 genomes]
rs6665320	0.91[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6682499	0.90[EUR][1000 genomes]
rs6682661	0.90[EUR][1000 genomes]
rs6682720	0.90[EUR][1000 genomes]
rs6684437	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs6684553	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6694699	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6698355	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs671830	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs672859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs673276	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs725907	0.82[EUR][1000 genomes]
rs7354819	0.88[EUR][1000 genomes]
rs7355030	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7511732	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7513876	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7514159	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7519465	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7535313	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs7536984	0.88[EUR][1000 genomes]
rs7537470	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs7547348	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7548097	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9583	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.99[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	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs564252	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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