Variant report

Variant	rs1256030
Chromosome Location	chr14:64747170-64747171
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	chr14:64746737..64749399-chr14:64750008..64752875,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10143616	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs10148269	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1152578	0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs1152579	0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs1152582	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1152588	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1152589	0.85[CHB][hapmap]
rs1152590	0.80[JPT][hapmap]
rs1152591	0.90[CHB][hapmap]
rs1152592	0.85[JPT][hapmap]
rs1152594	0.85[JPT][hapmap]
rs1255984	0.85[CHB][hapmap]
rs1255986	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs1256031	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1256033	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1256036	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256037	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256038	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1256039	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256040	1.00[CEU][hapmap];0.82[JPT][hapmap];0.98[EUR][1000 genomes]
rs1256041	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1256042	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1256043	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1256044	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]
rs1256045	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1256046	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1256048	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1256056	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1256059	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1256065	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1269056	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1271573	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2738413	0.90[CHB][hapmap]
rs3020445	0.81[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs6573552	0.85[EUR][1000 genomes]
rs6573553	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs7229	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs915057	0.95[CHB][hapmap]
rs928554	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs944046	0.84[ASN][1000 genomes]
rs944047	0.84[ASN][1000 genomes]
rs960069	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]
rs960070	0.92[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv1817597	chr14:64746287-64748557	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1256030	ESR2	cis	Skin Sun Exposed Lower leg	GTEx
rs1256030	SYNE2	cis	multi-tissue	Pritchard
rs1256030	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs1256030	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs1256030	ESR2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 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	chr14:64746000-64747600	Enhancers	HUVEC	blood vessel
4	chr14:64746400-64747200	Enhancers	Spleen	Spleen
5	chr14:64746400-64747200	Flanking Active TSS	K562	blood
6	chr14:64746400-64749200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr14:64746600-64747200	Enhancers	Pancreas	Pancrea
8	chr14:64746600-64747400	Enhancers	Dnd41	blood
9	chr14:64746600-64747400	Enhancers	Hela-S3	cervix
10	chr14:64746800-64747400	Enhancers	NHEK	skin
11	chr14:64747000-64748600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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