Variant report

Variant	rs1256044
Chromosome Location	chr14:64734027-64734028
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	chr14:64664909..64666611-chr14:64732886..64734717,2	MCF-7	breast:
2	chr14:64701273..64703199-chr14:64731826..64734576,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10143616	0.81[EUR][1000 genomes]
rs10148269	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10151658	0.88[MKK][hapmap]
rs1152577	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1152578	0.92[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1152579	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1152582	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1152586	0.86[AMR][1000 genomes]
rs1152588	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1152589	0.85[CHB][hapmap];0.82[GIH][hapmap]
rs1152590	0.80[JPT][hapmap]
rs1152591	0.90[CHB][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap]
rs1152592	0.85[JPT][hapmap]
rs1152594	0.85[JPT][hapmap]
rs1255984	0.85[CHB][hapmap];0.91[MKK][hapmap]
rs1255986	0.85[CHB][hapmap];0.80[JPT][hapmap];0.96[MKK][hapmap]
rs1256030	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1256031	0.85[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs1256033	0.85[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs1256036	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1256037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1256038	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1256039	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1256040	0.88[CEU][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes]
rs1256041	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1256042	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1256043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256046	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1256048	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1256056	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1256059	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1256065	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1269056	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1271573	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1760988	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2357479	0.82[CEU][hapmap]
rs2738413	0.90[CHB][hapmap];0.83[MEX][hapmap];0.88[YRI][hapmap]
rs3020445	0.96[CEU][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs3783736	0.85[GIH][hapmap]
rs7229	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs915057	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs928554	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs944046	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs944047	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs960069	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv456326	chr14:64420413-64754361	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv564905	chr14:64420413-64754361	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1256044	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs1256044	SYNE2	cis	multi-tissue	Pritchard
rs1256044	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs1256044	ESR2	cis	Skin Sun Exposed Lower leg	GTEx
rs1256044	MTHFD1	cis	parietal	SCAN
rs1256044	SYNE2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64727600-64741200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:64727600-64757600	Weak transcription	Ovary	ovary
3	chr14:64733200-64739000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr14:64733400-64736600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr14:64733600-64736200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr14:64733600-64736800	Weak transcription	Dnd41	blood
7	chr14:64734000-64734800	Strong transcription	Adipose Nuclei	Adipose
8	chr14:64734000-64735400	Strong transcription	Thymus	Thymus

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