Variant report

Variant	rs2987959
Chromosome Location	chr14:64832600-64832601
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10131195	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10145700	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10146204	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11158538	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12100642	0.81[EUR][1000 genomes]
rs28570137	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2983733	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2983736	0.81[EUR][1000 genomes]
rs2983738	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2983739	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2983741	0.85[EUR][1000 genomes]
rs2983742	0.87[EUR][1000 genomes]
rs2983746	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2983747	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2987958	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2987960	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2987961	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2987962	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2987963	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2987964	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2987965	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2987969	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2987970	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2987971	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2987972	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2987973	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2987974	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2987977	0.87[EUR][1000 genomes]
rs2987979	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2987982	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2987984	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3020436	0.81[EUR][1000 genomes]
rs3020438	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3020439	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3020441	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3020442	0.82[AMR][1000 genomes]
rs4902274	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57087457	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57351847	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7151163	0.86[EUR][1000 genomes]
rs8003153	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8007217	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8010584	0.85[EUR][1000 genomes]
rs8018032	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9323449	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];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	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
rs2987959	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs2987959	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs2987959	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs2987959	MTHFD1	cis	Artery Tibial	GTEx
rs2987959	MTHFD1	cis	Thyroid	GTEx

Chromatin state (count:6 , 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
6	chr14:64832600-64832800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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