Variant report

Variant	rs4490410
Chromosome Location	chr3:160893511-160893512
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160864038..160866583-chr3:160891018..160893791,2	MCF-7	breast:
2	chr3:160892333..160895194-chr3:160896982..160899442,2	MCF-7	breast:
3	chr3:160817475..160820143-chr3:160893422..160895281,2	MCF-7	breast:
4	chr3:160809965..160812767-chr3:160891424..160893829,2	MCF-7	breast:
5	chr3:160891061..160893820-chr3:160896787..160898326,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169255	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs12488037	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12488878	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs12494844	1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13318781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13319969	0.92[JPT][hapmap];0.82[AMR][1000 genomes]
rs13320863	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1471440	0.94[CHB][hapmap]
rs1599380	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1599382	0.82[CEU][hapmap]
rs1599391	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs163138	0.93[CHB][hapmap]
rs1947685	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1947686	0.92[JPT][hapmap]
rs1970834	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2061580	0.82[CEU][hapmap]
rs2231252	0.83[JPT][hapmap]
rs336544	0.94[CHB][hapmap]
rs336545	0.94[CHB][hapmap]
rs336546	0.94[CHB][hapmap]
rs336564	0.94[CHB][hapmap]
rs336565	0.94[CHB][hapmap]
rs336566	0.94[CHB][hapmap]
rs336574	0.94[CHB][hapmap]
rs336576	0.94[CHB][hapmap]
rs336587	0.93[CHB][hapmap]
rs336588	0.94[CHB][hapmap]
rs336592	0.94[CHB][hapmap]
rs35152606	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35446590	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36105583	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4270539	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4429651	0.83[ASN][1000 genomes]
rs4443220	0.83[JPT][hapmap]
rs4465984	1.00[JPT][hapmap]
rs4487256	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs62278031	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62278055	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62279860	0.83[ASN][1000 genomes]
rs62279861	0.83[ASN][1000 genomes]
rs62279862	0.81[ASN][1000 genomes]
rs6441353	0.83[JPT][hapmap]
rs6795977	0.83[JPT][hapmap]
rs6799805	0.82[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs731363	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73160351	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73160362	0.83[ASN][1000 genomes]
rs7622060	0.82[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs7634115	0.84[AMR][1000 genomes]
rs7649959	0.80[ASN][1000 genomes]
rs778651	0.82[CEU][hapmap]
rs778652	0.82[CEU][hapmap]
rs778655	0.86[CEU][hapmap]
rs898676	0.82[CEU][hapmap]
rs9290067	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9290068	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9290072	0.94[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs978933	0.94[CHB][hapmap]
rs9810737	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9811833	0.94[CHB][hapmap]
rs9812083	0.94[CHB][hapmap]
rs9817747	0.86[ASN][1000 genomes]
rs9818516	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9824308	0.83[JPT][hapmap]
rs9824501	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9825118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827833	0.94[CHB][hapmap]
rs9828189	0.94[CHB][hapmap]
rs9828205	0.93[EUR][1000 genomes]
rs9828231	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs9831725	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9836074	0.94[EUR][1000 genomes]
rs9836094	0.83[ASN][1000 genomes]
rs9839404	0.94[CHB][hapmap]
rs9842281	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846316	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs9857946	0.92[ASN][1000 genomes]
rs9858399	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862258	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9876553	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs9878365	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4490410	DNMT1	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160893000-160894000	Enhancers	HUVEC	blood vessel

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