Variant report

Variant	rs2238195
Chromosome Location	chr14:72804080-72804081
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	chr14:72800415..72803046-chr14:72803047..72804639,2	MCF-7	breast:
2	chr14:72794559..72797059-chr14:72803417..72805844,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10146126	0.81[AMR][1000 genomes]
rs10149207	0.82[YRI][hapmap]
rs11620677	0.89[ASW][hapmap];0.87[CHD][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes]
rs1356842	0.83[CEU][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1402063	0.87[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes]
rs1402064	0.87[CHB][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.85[AMR][1000 genomes]
rs1996661	0.88[ASW][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes]
rs2090736	0.87[AMR][1000 genomes]
rs2139596	0.83[CEU][hapmap]
rs2190509	0.83[CEU][hapmap]
rs2222311	0.94[ASW][hapmap];0.82[CEU][hapmap];0.88[GIH][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes]
rs2238206	0.82[YRI][hapmap]
rs2238207	0.80[MEX][hapmap];0.82[YRI][hapmap]
rs2239244	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2239246	0.80[CHB][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2250557	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2250666	0.87[CHB][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2529459	0.83[CEU][hapmap]
rs2529474	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2529476	0.86[AMR][1000 genomes]
rs2681729	0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2681732	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2681738	0.82[AMR][1000 genomes]
rs2681739	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2681740	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2681750	0.83[CEU][hapmap]
rs2681770	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7151952	0.82[YRI][hapmap]
rs765221	0.94[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs847331	0.83[ASW][hapmap];0.82[YRI][hapmap]
rs847334	0.83[CEU][hapmap]
rs847346	0.90[GIH][hapmap]
rs847348	0.83[AMR][1000 genomes]
rs847349	0.83[AMR][1000 genomes]
rs847350	0.82[AMR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2238195	COQ6	cis	parietal	SCAN
rs2238195	NEK9	cis	cerebellum	SCAN
rs2238195	DCAF4	cis	parietal	SCAN

Chromatin state (count:3 , 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	chr14:72801000-72807400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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