Variant report

Variant	rs1256095
Chromosome Location	chr14:64837161-64837162
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	chr14:64836307..64837945-chr14:64969912..64971626,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000126804	Chromatin interaction
ENSG00000089775	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10131195	0.82[EUR][1000 genomes]
rs1076991	0.80[MEX][hapmap];0.80[TSI][hapmap]
rs11158538	0.80[TSI][hapmap]
rs12434608	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1256093	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1256097	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1256099	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1256100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1256101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1256102	0.99[EUR][1000 genomes]
rs1256107	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1256108	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1256109	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1256110	0.91[CEU][hapmap]
rs1256111	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1256112	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.96[ASN][1000 genomes]
rs1256113	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1262246	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1270057	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12886138	0.88[ASN][1000 genomes]
rs12889097	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12894546	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28570137	0.82[EUR][1000 genomes]
rs2987958	0.82[EUR][1000 genomes]
rs2987960	0.83[EUR][1000 genomes]
rs2987961	0.83[EUR][1000 genomes]
rs2987963	0.82[EUR][1000 genomes]
rs2987964	0.83[EUR][1000 genomes]
rs2987969	0.89[ASW][hapmap];0.89[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs2987970	0.83[EUR][1000 genomes]
rs2987971	0.83[EUR][1000 genomes]
rs2987982	0.83[EUR][1000 genomes]
rs3020438	0.80[EUR][1000 genomes]
rs3020439	0.81[EUR][1000 genomes]
rs3020441	0.82[EUR][1000 genomes]
rs3020445	0.80[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs35020344	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36016358	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[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]
rs8011386	1.00[YRI][hapmap]
rs8018032	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1256095	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs1256095	MTHFD1	cis	cerebellum	SCAN
rs1256095	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs1256095	MTHFD1	cis	parietal	SCAN
rs1256095	MTHFD1	cis	Thyroid	GTEx
rs1256095	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs1256095	KCNH5	cis	parietal	SCAN

Chromatin state (count:1 , 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

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