Variant report

Variant	rs2217649
Chromosome Location	chr5:108474166-108474167
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10037370	0.96[ASN][1000 genomes]
rs10040959	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10043540	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs10056058	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10063845	0.86[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10070411	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10085093	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10477440	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10477944	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10477945	0.86[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10477946	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10477947	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10477948	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10477949	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10477952	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11746665	0.89[EUR][1000 genomes]
rs17450345	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs17450387	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17450455	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17473391	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17534626	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2195944	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2416198	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2416200	0.95[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28699553	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3816024	0.91[CHD][hapmap]
rs4957567	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4957798	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4957799	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55930293	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55953478	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56227556	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57196331	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57960033	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59337218	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6872780	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73779027	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73779047	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73779050	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73779051	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73779130	0.86[EUR][1000 genomes]
rs73779135	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9285864	0.83[LWK][hapmap];0.84[MKK][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes]
rs9326759	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9326760	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9326762	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830443	chr5:108326491-108496723	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv882692	chr5:108391660-108474166	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882693	chr5:108391660-108502493	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv882694	chr5:108391660-108524416	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv4953	chr5:108443905-108488747	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1027163	chr5:108445447-108839913	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv2756048	chr5:108448101-108542101	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2217649	APC	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108442000-108497400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:108468400-108478600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr5:108468600-108477000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:108468800-108521800	Weak transcription	Aorta	Aorta
5	chr5:108469200-108475200	Weak transcription	Primary T cells from cord blood	blood
6	chr5:108469600-108478600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:108470000-108497000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:108470400-108482200	Weak transcription	HSMM	muscle
9	chr5:108470600-108477200	Weak transcription	Ovary	ovary
10	chr5:108473200-108477200	Weak transcription	NHLF	lung
11	chr5:108473800-108488400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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