Variant report

Variant	rs3020436
Chromosome Location	chr14:64842570-64842571
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64841399..64842966-chr14:64852700..64855296,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100714	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10131195	0.84[EUR][1000 genomes]
rs10145700	0.96[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1076991	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs11158538	0.92[ASW][hapmap];0.89[CEU][hapmap];0.96[GIH][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.94[EUR][1000 genomes]
rs12100642	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256093	0.83[MEX][hapmap];0.85[TSI][hapmap]
rs28570137	0.85[EUR][1000 genomes]
rs2983733	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2983736	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2983738	0.89[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2983739	0.82[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2983741	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2983742	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2983746	0.99[EUR][1000 genomes]
rs2983747	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2987958	0.84[EUR][1000 genomes]
rs2987959	0.81[EUR][1000 genomes]
rs2987960	0.85[EUR][1000 genomes]
rs2987961	0.85[EUR][1000 genomes]
rs2987962	0.89[EUR][1000 genomes]
rs2987963	0.85[EUR][1000 genomes]
rs2987964	0.85[EUR][1000 genomes]
rs2987969	0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs2987970	0.85[EUR][1000 genomes]
rs2987971	0.85[EUR][1000 genomes]
rs2987973	0.92[EUR][1000 genomes]
rs2987974	0.84[EUR][1000 genomes]
rs2987977	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2987979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2987982	0.85[EUR][1000 genomes]
rs2987984	0.91[EUR][1000 genomes]
rs3020438	0.82[EUR][1000 genomes]
rs3020439	0.84[EUR][1000 genomes]
rs3020441	0.85[EUR][1000 genomes]
rs3020442	0.95[EUR][1000 genomes]
rs35020344	0.83[MEX][hapmap];0.87[TSI][hapmap]
rs4902274	0.81[EUR][1000 genomes]
rs57087457	0.93[EUR][1000 genomes]
rs7151163	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8003153	0.85[EUR][1000 genomes]
rs8007217	0.86[EUR][1000 genomes]
rs8010584	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8018032	0.84[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3020436	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs3020436	MTHFD1	cis	parietal	SCAN
rs3020436	MTHFD1	cis	cerebellum	SCAN
rs3020436	KCNH5	cis	parietal	SCAN
rs3020436	MTHFD1	cis	Thyroid	GTEx
rs3020436	MTHFD1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:2 , 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

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