Variant report

Variant	rs3020438
Chromosome Location	chr14:64814942-64814943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:64810311..64815696-chr14:64852502..64857226,7	MCF-7	breast:
2	chr14:64813513..64815077-chr14:64817332..64820042,2	K562	blood:
3	chr14:64814931..64817435-chr14:64969871..64972110,2	MCF-7	breast:
4	chr14:64813453..64815702-chr14:64970879..64973824,2	K562	blood:

Variant related genes	Relation type
ENSG00000100714	Chromatin interaction
ENSG00000089775	Chromatin interaction
ENSG00000126804	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10131195	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10145700	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10146204	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11158538	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12100642	0.82[EUR][1000 genomes]
rs1256095	0.80[EUR][1000 genomes]
rs1256100	0.80[EUR][1000 genomes]
rs1256102	0.81[EUR][1000 genomes]
rs1256107	0.80[EUR][1000 genomes]
rs1256108	0.80[EUR][1000 genomes]
rs1256111	0.80[EUR][1000 genomes]
rs1262246	0.80[EUR][1000 genomes]
rs28570137	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2983733	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2983736	0.82[EUR][1000 genomes]
rs2983738	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2983739	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2983741	0.86[EUR][1000 genomes]
rs2983742	0.88[EUR][1000 genomes]
rs2983746	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2983747	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2987958	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2987959	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2987960	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2987961	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2987962	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2987963	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2987964	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2987965	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2987969	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2987970	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2987971	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2987972	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2987973	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2987974	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2987977	0.90[EUR][1000 genomes]
rs2987979	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2987982	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2987984	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3020436	0.82[EUR][1000 genomes]
rs3020439	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020441	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020442	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4902274	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57087457	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57351847	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7151163	0.87[EUR][1000 genomes]
rs8003153	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8007217	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8010584	0.86[EUR][1000 genomes]
rs8018032	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9323449	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3020438	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs3020438	MTHFD1	cis	Artery Tibial	GTEx
rs3020438	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs3020438	MTHFD1	cis	Thyroid	GTEx
rs3020438	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 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

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