Variant report

Variant	rs960069
Chromosome Location	chr14:64745002-64745003
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	chr14:64742475..64745477-chr14:64747736..64750527,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140009	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10148269	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];0.97[ASN][1000 genomes]
rs1152577	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1152578	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1152579	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1152582	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1152586	0.87[AMR][1000 genomes]
rs1152588	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1152589	0.89[CHB][hapmap]
rs1152590	0.83[CHB][hapmap]
rs1152591	0.94[CHB][hapmap];0.88[YRI][hapmap]
rs1152592	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs1152594	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs1152601	0.83[CHB][hapmap]
rs1255984	0.89[CHB][hapmap]
rs1255986	0.89[CHB][hapmap]
rs1255990	0.83[CHB][hapmap]
rs1256030	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256031	0.83[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs1256033	0.83[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs1256036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256037	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256038	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];0.98[ASN][1000 genomes]
rs1256039	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256040	0.86[CEU][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes]
rs1256041	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1256042	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1256043	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1256044	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]
rs1256045	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1256046	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1256048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1256056	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1256059	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1256065	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1262242	0.83[CHB][hapmap]
rs1269056	1.00[CEU][hapmap];0.94[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];1.00[ASN][1000 genomes]
rs1271573	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1760988	0.89[AMR][1000 genomes]
rs2357479	0.81[AMR][1000 genomes]
rs2738413	0.94[CHB][hapmap];0.88[YRI][hapmap]
rs3020445	0.95[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs7229	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs872227	0.83[CHB][hapmap]
rs915057	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes]
rs928554	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs944046	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs944047	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs960070	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv1307	chr14:64742037-64787315	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs960069	ESR2	cis	Skin Sun Exposed Lower leg	GTEx
rs960069	SYNE2	cis	multi-tissue	Pritchard
rs960069	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs960069	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs960069	SYNE2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64727600-64757600	Weak transcription	Ovary	ovary
2	chr14:64735400-64757200	Weak transcription	Thymus	Thymus
3	chr14:64743800-64745200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr14:64743800-64745600	Enhancers	HUVEC	blood vessel
5	chr14:64744800-64745800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr14:64744800-64746200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr14:64745000-64745400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr14:64745000-64745600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr14:64745000-64746000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr14:64745000-64746000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr14:64745000-64746000	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr14:64745000-64746800	Enhancers	H1 Cell Line	embryonic stem cell

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