Variant report

Variant	rs1256040
Chromosome Location	chr14:64738394-64738395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10143616	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs10148269	0.88[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs1256030	1.00[CEU][hapmap];0.82[JPT][hapmap];0.98[EUR][1000 genomes]
rs1256031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1256033	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256036	0.88[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs1256037	0.88[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs1256038	0.88[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs1256039	0.93[EUR][1000 genomes]
rs1256041	0.92[EUR][1000 genomes]
rs1256042	0.93[EUR][1000 genomes]
rs1256043	0.86[CEU][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes]
rs1256044	0.88[CEU][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes]
rs1256045	0.88[CEU][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs1256046	0.93[EUR][1000 genomes]
rs1256048	0.88[CEU][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs1256056	0.80[CEU][hapmap];0.87[EUR][1000 genomes]
rs1256059	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs1256061	0.84[JPT][hapmap]
rs1256065	0.82[EUR][1000 genomes]
rs1269056	0.88[CEU][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes]
rs1271573	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs3020445	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs6573552	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6573553	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs7229	0.80[CEU][hapmap]
rs960069	0.86[CEU][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes]
rs960070	0.92[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv456326	chr14:64420413-64754361	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv564905	chr14:64420413-64754361	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1256040	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs1256040	SYNE2	cis	multi-tissue	Pritchard
rs1256040	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs1256040	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs1256040	ESR2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64727600-64741200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:64727600-64757600	Weak transcription	Ovary	ovary
3	chr14:64733200-64739000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr14:64735400-64757200	Weak transcription	Thymus	Thymus

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