Variant report

Variant	rs1402064
Chromosome Location	chr14:72802959-72802960
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	chr14:72800415..72803046-chr14:72803047..72804639,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10146126	0.81[CHB][hapmap]
rs1072165	0.82[EUR][1000 genomes]
rs11620677	1.00[CEU][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1356842	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1402063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996661	0.93[CHB][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2090736	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2139596	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2190509	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2222311	0.93[CHB][hapmap];0.80[GIH][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2238195	0.87[CHB][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.85[AMR][1000 genomes]
rs2239244	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2239246	0.87[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2250557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2250666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2529458	0.85[EUR][1000 genomes]
rs2529459	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2529465	0.85[EUR][1000 genomes]
rs2529474	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2529476	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2681729	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2681732	0.82[AMR][1000 genomes]
rs2681738	1.00[CEU][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2681739	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2681750	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2681756	0.82[EUR][1000 genomes]
rs2681758	0.84[EUR][1000 genomes]
rs2681760	0.85[EUR][1000 genomes]
rs2681763	0.84[EUR][1000 genomes]
rs2681770	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs765221	0.87[CHB][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs769148	0.86[CEU][hapmap]
rs847325	0.85[CEU][hapmap]
rs847329	0.86[CEU][hapmap]
rs847330	1.00[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs847334	0.85[CEU][hapmap];0.82[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	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv948800	chr14:72462557-73150701	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
3	esv2757573	chr14:72802736-72819684	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv2759995	chr14:72802736-72819684	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1402064	C14orf115	cis	cerebellum	SCAN
rs1402064	PI16	trans	cerebellum	SCAN
rs1402064	C14orf43	cis	cerebellum	SCAN
rs1402064	DCAF4	cis	parietal	SCAN
rs1402064	NEK9	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72797600-72804800	Enhancers	Fetal Lung	lung
2	chr14:72799200-72804200	Weak transcription	Spleen	Spleen
3	chr14:72801000-72803000	Weak transcription	Fetal Stomach	stomach
4	chr14:72801000-72807400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr14:72801400-72803800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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