Variant report

Variant	rs17166099
Chromosome Location	chr5:97903140-97903141
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11953303	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12187587	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17132958	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17132963	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17166146	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17166151	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17166174	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17842412	0.81[EUR][1000 genomes]
rs2053679	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6595958	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6595959	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6596179	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67468861	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6877381	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878913	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886015	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6890353	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72771755	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72771766	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72771780	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72771781	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72771783	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7701903	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711174	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7712835	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732069	1.00[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	nsv882412	chr5:97796120-97953719	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1016611	chr5:97873846-98035559	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv537816	chr5:97873846-98035559	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1029509	chr5:97888644-98040172	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17166099	SLCO4C1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:97893000-97905200	Weak transcription	NHLF	lung
2	chr5:97900000-97905200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr5:97900400-97903800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:97900600-97906400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:97900800-97906400	Weak transcription	Fetal Intestine Large	intestine
6	chr5:97902800-97906400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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