Variant report

Variant	rs659061
Chromosome Location	chr1:59024435-59024436
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59010806..59014775-chr1:59020178..59025032,4	MCF-7	breast:
2	chr1:59005153..59007258-chr1:59023962..59025940,2	K562	blood:
3	chr1:59023125..59024763-chr1:59041527..59043694,2	MCF-7	breast:
4	chr1:59010754..59013570-chr1:59022178..59025066,2	K562	blood:

Variant related genes	Relation type
ENSG00000162600	Chromatin interaction
ENSG00000184292	Chromatin interaction
ENSG00000173406	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10458559	0.91[CEU][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10789064	0.91[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10789065	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10789066	0.91[CEU][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10789067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10889098	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10889100	0.91[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10889101	0.81[CEU][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1109895	0.82[CEU][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1109896	0.89[CEU][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11207237	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11207250	0.95[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11207251	0.91[CEU][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11207252	0.91[CEU][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11207253	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11207254	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11581395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12030713	0.95[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12124662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12125391	0.91[CEU][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12142098	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1388981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1775002	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2087799	0.91[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs232822	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs232826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs232827	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs232830	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs232841	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs232842	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs232844	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs232847	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs232848	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs232849	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2406784	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3087585	0.95[CEU][hapmap]
rs338225	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3551	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs486463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4912195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4912344	0.87[ASN][1000 genomes]
rs525929	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs562166	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs584579	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs602579	0.95[CEU][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs603031	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61779295	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61779296	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs620342	0.91[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs627218	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6587819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6587820	0.91[CEU][hapmap]
rs6587828	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6656025	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6667614	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6667703	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs6687324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs672359	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67639631	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7355165	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs7355166	0.82[EUR][1000 genomes]
rs7517424	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7520008	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7536230	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7544032	0.87[ASN][1000 genomes]
rs7546900	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7547036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs905567	0.91[CEU][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9660901	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs659061	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL
rs659061	TACSTD2	cis	Thyroid	GTEx
rs659061	TACSTD2	cis	Whole Blood	GTEx

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

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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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