Variant report

Variant	rs2987960
Chromosome Location	chr14:64831871-64831872
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10131195	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10145700	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10146204	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158538	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12100642	0.85[EUR][1000 genomes]
rs1256095	0.83[EUR][1000 genomes]
rs1256097	0.82[EUR][1000 genomes]
rs1256099	0.82[EUR][1000 genomes]
rs1256100	0.83[EUR][1000 genomes]
rs1256101	0.82[EUR][1000 genomes]
rs1256102	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1256107	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1256108	0.83[EUR][1000 genomes]
rs1256109	0.82[EUR][1000 genomes]
rs1256111	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1262246	0.83[EUR][1000 genomes]
rs1270057	0.82[EUR][1000 genomes]
rs28570137	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2983733	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2983736	0.85[EUR][1000 genomes]
rs2983738	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2983739	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2983741	0.89[EUR][1000 genomes]
rs2983742	0.91[EUR][1000 genomes]
rs2983746	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2983747	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2987958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987959	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2987961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987962	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2987963	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987964	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2987965	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987969	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987970	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2987971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987972	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987973	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2987974	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2987977	0.91[EUR][1000 genomes]
rs2987979	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2987982	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987984	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3020436	0.85[EUR][1000 genomes]
rs3020438	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3020439	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3020441	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3020442	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4902274	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57087457	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57351847	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7151163	0.90[EUR][1000 genomes]
rs8003153	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8007217	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8010584	0.89[EUR][1000 genomes]
rs8018032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9323449	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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
rs2987960	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs2987960	MTHFD1	cis	Thyroid	GTEx
rs2987960	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs2987960	MTHFD1	cis	Artery Tibial	GTEx
rs2987960	SYNE2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 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	chr14:64830800-64832000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr14:64831200-64832400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr14:64831400-64832200	Enhancers	NHDF-Ad	bronchial
8	chr14:64831600-64832400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr14:64831600-64832600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr14:64831600-64832600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr14:64831600-64832600	Enhancers	NHEK	skin
12	chr14:64831800-64832000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr14:64831800-64832000	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links