Variant report

Variant	rs12894546
Chromosome Location	chr14:64849957-64849958
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:64849072..64851783-chr14:64852563..64854681,2	K562	blood:
2	chr14:64849395..64851590-chr14:64852646..64856063,3	MCF-7	breast:
3	chr14:64849483..64852419-chr14:64853173..64856118,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100714	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11158538	0.82[EUR][1000 genomes]
rs12434608	0.97[EUR][1000 genomes]
rs1256093	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256095	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1256097	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1256099	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1256100	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1256101	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1256102	0.90[EUR][1000 genomes]
rs1256107	0.89[EUR][1000 genomes]
rs1256108	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1256109	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1256111	0.89[EUR][1000 genomes]
rs1256112	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1256113	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1262246	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1270057	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12886138	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12889097	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2983741	0.82[EUR][1000 genomes]
rs2983742	0.84[EUR][1000 genomes]
rs35020344	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36016358	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243628	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57087457	0.83[EUR][1000 genomes]
rs7151163	0.83[EUR][1000 genomes]
rs8010584	0.82[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
rs12894546	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs12894546	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs12894546	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs12894546	MTHFD1	cis	Skin Sun Exposed Lower leg	GTEx
rs12894546	MTHFD1	cis	Thyroid	GTEx

Chromatin state (count:7 , 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
5	chr14:64847000-64853000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr14:64848600-64852400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr14:64849400-64854000	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links