Variant report

Variant	rs5762656
Chromosome Location	chr22:28877335-28877336
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	chr22:28877288..28878029-chr8:118385775..118386611,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10427676	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs134527	0.90[JPT][hapmap]
rs134544	0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs17412920	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17504822	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2346395	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs5752728	0.89[ASN][1000 genomes]
rs5752729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5752745	0.85[CEU][hapmap]
rs5752746	0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs5752766	0.90[EUR][1000 genomes]
rs5762572	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5762604	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5762622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5762654	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5762664	1.00[LWK][hapmap]
rs5762666	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5762686	1.00[ASW][hapmap];0.84[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs5762736	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5762737	0.81[CEU][hapmap]
rs695388	0.85[JPT][hapmap]
rs7286920	0.92[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7288416	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73168176	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs738199	0.85[CEU][hapmap]
rs9306455	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9306458	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9608677	1.00[ASW][hapmap];0.85[MEX][hapmap]
rs9608692	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9613609	0.94[ASN][1000 genomes]
rs9613617	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9613630	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613639	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9613658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][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	nsv1067544	chr22:28755418-29055246	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv544674	chr22:28755418-29055246	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv588880	chr22:28807277-29001789	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs5762656	C22orf13	cis	parietal	SCAN
rs5762656	MTFP1	cis	cerebellum	SCAN
rs5762656	TTC28	cis	cerebellum	SCAN
rs5762656	CABP7	cis	cerebellum	SCAN
rs5762656	TFIP11	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28861600-28880200	Weak transcription	Ovary	ovary
2	chr22:28874000-28878600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:28875000-28879000	Enhancers	Fetal Brain Male	brain
4	chr22:28875200-28878000	Enhancers	Fetal Lung	lung
5	chr22:28875800-28878400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr22:28876000-28878000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr22:28876000-28878000	Enhancers	Brain Germinal Matrix	brain
8	chr22:28876200-28878000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr22:28876600-28878000	Enhancers	Fetal Brain Female	brain
10	chr22:28876800-28877600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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