Variant report

Variant	rs2983733
Chromosome Location	chr14:64849415-64849416
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Variant related genes	Relation type
ENSG00000100714	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10131195	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10145700	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1076991	1.00[ASW][hapmap];0.89[CEU][hapmap];0.91[GIH][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs11158537	0.99[ASN][1000 genomes]
rs11158538	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11158539	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12100642	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1256093	0.85[TSI][hapmap]
rs28570137	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2983736	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.99[EUR][1000 genomes]
rs2983738	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983739	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2983741	0.92[EUR][1000 genomes]
rs2983742	0.93[EUR][1000 genomes]
rs2983746	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2983747	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2987958	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2987959	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2987960	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2987961	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2987962	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2987963	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2987964	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2987969	0.83[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2987970	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2987971	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2987973	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2987974	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2987977	0.91[EUR][1000 genomes]
rs2987979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2987982	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2987984	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3020436	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]
rs3020438	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3020439	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3020441	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3020442	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35020344	0.87[TSI][hapmap]
rs3783731	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4902274	0.82[EUR][1000 genomes]
rs56029832	0.96[ASN][1000 genomes]
rs57087457	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57845486	0.99[ASN][1000 genomes]
rs7151163	0.89[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs72722376	0.99[ASN][1000 genomes]
rs8003153	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8006686	0.89[ASN][1000 genomes]
rs8007217	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8010584	0.91[EUR][1000 genomes]
rs8011839	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs8015898	0.83[ASN][1000 genomes]
rs8018032	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8020827	0.82[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2983733	MTHFD1	cis	Thyroid	GTEx
rs2983733	HNMT	trans	lymphoblastoid	seeQTL

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

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