Variant report

Variant	rs1256099
Chromosome Location	chr14:64832590-64832591
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10131195	0.81[EUR][1000 genomes]
rs12434608	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1256093	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1256095	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1256097	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1256100	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1256101	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1256102	0.98[EUR][1000 genomes]
rs1256107	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1256108	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1256109	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1256111	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1256112	0.97[ASN][1000 genomes]
rs1256113	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1262246	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1270057	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12886138	0.89[ASN][1000 genomes]
rs12889097	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12894546	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28570137	0.81[EUR][1000 genomes]
rs2987958	0.81[EUR][1000 genomes]
rs2987960	0.82[EUR][1000 genomes]
rs2987961	0.82[EUR][1000 genomes]
rs2987963	0.81[EUR][1000 genomes]
rs2987964	0.82[EUR][1000 genomes]
rs2987969	0.81[EUR][1000 genomes]
rs2987970	0.82[EUR][1000 genomes]
rs2987971	0.82[EUR][1000 genomes]
rs2987982	0.82[EUR][1000 genomes]
rs3020439	0.80[EUR][1000 genomes]
rs3020441	0.81[EUR][1000 genomes]
rs3020445	0.81[ASN][1000 genomes]
rs35020344	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36016358	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4243628	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8003153	0.81[EUR][1000 genomes]
rs8007217	0.80[EUR][1000 genomes]
rs8018032	0.81[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1256099	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs1256099	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs1256099	MTHFD1	cis	Skin Sun Exposed Lower leg	GTEx
rs1256099	MTHFD1	cis	Thyroid	GTEx
rs1256099	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64816400-64853400	Weak transcription	Primary B cells from cord blood	blood
2	chr14:64831600-64832600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr14:64831600-64832600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr14:64831600-64832600	Enhancers	NHEK	skin
5	chr14:64832000-64832800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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