Variant report

Variant	rs3020445
Chromosome Location	chr14:64788644-64788645
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	chr14:64787867..64791213-chr14:64803202..64806273,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214770	Chromatin interaction
ENSG00000140009	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10148269	0.96[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs1152578	0.88[CEU][hapmap]
rs1152579	0.83[CEU][hapmap]
rs1152582	0.88[CEU][hapmap]
rs1152588	0.88[CEU][hapmap]
rs1152589	0.88[MKK][hapmap]
rs1256030	0.81[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs1256031	0.81[CEU][hapmap];0.83[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs1256033	0.81[CEU][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs1256036	0.96[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs1256037	0.96[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs1256038	0.96[CEU][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs1256039	0.89[EUR][1000 genomes]
rs1256040	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs1256041	0.87[EUR][1000 genomes]
rs1256042	0.89[EUR][1000 genomes]
rs1256043	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs1256044	0.96[CEU][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs1256045	0.96[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs1256046	0.89[EUR][1000 genomes]
rs1256048	0.96[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs1256056	0.88[CEU][hapmap];0.84[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs1256059	0.88[CEU][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs1256065	0.85[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap]
rs1256093	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs1256095	0.80[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs1256099	0.81[ASN][1000 genomes]
rs1256100	0.82[ASN][1000 genomes]
rs1256101	0.82[ASN][1000 genomes]
rs1256108	0.83[ASN][1000 genomes]
rs1256109	0.83[ASN][1000 genomes]
rs1256112	0.80[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1256113	0.83[ASN][1000 genomes]
rs1262246	0.82[ASN][1000 genomes]
rs1269056	0.96[CEU][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs1270057	0.81[ASN][1000 genomes]
rs1271573	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs12886138	0.82[AFR][1000 genomes]
rs2357479	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35020344	0.90[JPT][hapmap]
rs6573553	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs7229	0.88[CEU][hapmap];0.84[GIH][hapmap];0.94[MKK][hapmap]
rs915057	0.84[CEU][hapmap];0.84[GIH][hapmap]
rs928554	0.84[CEU][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap]
rs960069	0.95[CEU][hapmap];0.81[JPT][hapmap];0.89[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	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3020445	MTHFD1	cis	parietal	SCAN
rs3020445	ESR2	cis	Skin Sun Exposed Lower leg	GTEx
rs3020445	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs3020445	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs3020445	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs3020445	SYNE2	cis	multi-tissue	Pritchard

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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