Variant report

Variant	rs2983742
Chromosome Location	chr14:64844827-64844828
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10131195	0.90[EUR][1000 genomes]
rs10145700	0.93[EUR][1000 genomes]
rs10146204	0.84[EUR][1000 genomes]
rs11158538	0.98[EUR][1000 genomes]
rs12100642	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12434608	0.82[EUR][1000 genomes]
rs1256093	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12894546	0.84[EUR][1000 genomes]
rs28570137	0.90[EUR][1000 genomes]
rs2983733	0.93[EUR][1000 genomes]
rs2983736	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2983738	0.92[EUR][1000 genomes]
rs2983739	0.93[EUR][1000 genomes]
rs2983741	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2983746	0.93[EUR][1000 genomes]
rs2983747	0.87[EUR][1000 genomes]
rs2987958	0.90[EUR][1000 genomes]
rs2987959	0.87[EUR][1000 genomes]
rs2987960	0.91[EUR][1000 genomes]
rs2987961	0.91[EUR][1000 genomes]
rs2987962	0.84[EUR][1000 genomes]
rs2987963	0.90[EUR][1000 genomes]
rs2987964	0.91[EUR][1000 genomes]
rs2987965	0.84[EUR][1000 genomes]
rs2987969	0.90[EUR][1000 genomes]
rs2987970	0.91[EUR][1000 genomes]
rs2987971	0.91[EUR][1000 genomes]
rs2987972	0.85[EUR][1000 genomes]
rs2987973	0.87[EUR][1000 genomes]
rs2987974	0.90[EUR][1000 genomes]
rs2987977	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2987979	0.93[EUR][1000 genomes]
rs2987982	0.91[EUR][1000 genomes]
rs2987984	0.86[EUR][1000 genomes]
rs3020436	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3020438	0.88[EUR][1000 genomes]
rs3020439	0.89[EUR][1000 genomes]
rs3020441	0.90[EUR][1000 genomes]
rs3020442	0.90[EUR][1000 genomes]
rs35020344	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36016358	0.84[EUR][1000 genomes]
rs4902274	0.87[EUR][1000 genomes]
rs57087457	0.99[EUR][1000 genomes]
rs57351847	0.83[EUR][1000 genomes]
rs7144136	0.88[ASN][1000 genomes]
rs7151163	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8003153	0.90[EUR][1000 genomes]
rs8007217	0.91[EUR][1000 genomes]
rs8010584	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8018032	0.90[EUR][1000 genomes]
rs9323449	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	esv3416507	chr14:64844547-64845074	Weak transcription	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2983742	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs2983742	MTHFD1	cis	Skin Sun Exposed Lower leg	GTEx
rs2983742	MTHFD1	cis	Artery Tibial	GTEx
rs2983742	MTHFD1	cis	Thyroid	GTEx
rs2983742	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 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	chr14:64839200-64853800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr14:64843800-64853400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr14:64844200-64854000	Weak transcription	Ovary	ovary

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