Variant report

Variant	rs1256109
Chromosome Location	chr14:64818496-64818497
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:64803501..64806000-chr14:64816741..64818723,2	K562	blood:
2	chr14:64817061..64818611-chr14:64854457..64856600,2	MCF-7	breast:
3	chr14:64804739..64807638-chr14:64817881..64820588,2	MCF-7	breast:
4	chr14:64813513..64815077-chr14:64817332..64820042,2	K562	blood:

Variant related genes	Relation type
ENSG00000100714	Chromatin interaction
ENSG00000140009	Chromatin interaction
ENSG00000214770	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10131195	0.81[EUR][1000 genomes]
rs12434608	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1256093	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1256095	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1256097	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1256099	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1256100	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256101	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256102	0.98[EUR][1000 genomes]
rs1256107	0.89[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1256108	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256111	0.89[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1256112	0.99[ASN][1000 genomes]
rs1256113	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1262246	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1270057	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12886138	0.88[ASN][1000 genomes]
rs12889097	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12894546	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28570137	0.83[EUR][1000 genomes]
rs2987958	0.81[EUR][1000 genomes]
rs2987960	0.82[EUR][1000 genomes]
rs2987961	0.82[EUR][1000 genomes]
rs2987963	0.82[EUR][1000 genomes]
rs2987964	0.82[EUR][1000 genomes]
rs2987969	0.81[EUR][1000 genomes]
rs2987970	0.82[EUR][1000 genomes]
rs2987971	0.82[EUR][1000 genomes]
rs2987982	0.82[EUR][1000 genomes]
rs3020439	0.81[EUR][1000 genomes]
rs3020441	0.82[EUR][1000 genomes]
rs3020445	0.83[ASN][1000 genomes]
rs35020344	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36016358	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4243628	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8003153	0.82[EUR][1000 genomes]
rs8007217	0.81[EUR][1000 genomes]
rs8018032	0.81[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	nsv84862	chr14:64813942-64818537	Weak transcription	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1256109	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs1256109	MTHFD1	cis	Thyroid	GTEx
rs1256109	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs1256109	ESR2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64806200-64819200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr14:64807600-64827400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr14:64813200-64822200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr14:64816400-64853400	Weak transcription	Primary B cells from cord blood	blood

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