Variant report

Variant	rs2987962
Chromosome Location	chr14:64831570-64831571
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10131195	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10145700	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10146204	0.86[EUR][1000 genomes]
rs11158537	0.90[ASN][1000 genomes]
rs11158538	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12100642	0.89[EUR][1000 genomes]
rs28570137	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2983733	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2983736	0.89[EUR][1000 genomes]
rs2983738	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2983739	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2983741	0.83[EUR][1000 genomes]
rs2983742	0.84[EUR][1000 genomes]
rs2983746	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2983747	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2987958	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2987959	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2987960	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2987961	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2987963	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2987964	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2987965	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2987969	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2987970	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2987971	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2987972	0.86[EUR][1000 genomes]
rs2987973	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2987974	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2987977	0.95[EUR][1000 genomes]
rs2987979	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2987982	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2987984	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020436	0.89[EUR][1000 genomes]
rs3020438	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3020439	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3020441	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3020442	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3783731	0.86[ASN][1000 genomes]
rs4902274	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56029832	0.87[ASN][1000 genomes]
rs57087457	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57351847	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57845486	0.90[ASN][1000 genomes]
rs7151163	0.85[EUR][1000 genomes]
rs72722376	0.90[ASN][1000 genomes]
rs8003153	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8006686	0.81[ASN][1000 genomes]
rs8007217	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8010584	0.82[EUR][1000 genomes]
rs8011839	0.81[ASN][1000 genomes]
rs8018032	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9323449	0.81[AMR][1000 genomes];0.86[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2987962	MTHFD1	cis	Thyroid	GTEx
rs2987962	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 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	chr14:64829800-64832000	Enhancers	K562	blood
3	chr14:64830000-64832400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr14:64830000-64832400	Enhancers	Osteobl	bone
5	chr14:64830400-64831600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr14:64830400-64831600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr14:64830600-64831600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr14:64830600-64831600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr14:64830600-64831600	Weak transcription	NHEK	skin
10	chr14:64830800-64831800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr14:64830800-64831800	Weak transcription	NH-A	brain
12	chr14:64830800-64832000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr14:64831200-64832400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr14:64831400-64832200	Enhancers	NHDF-Ad	bronchial

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