Variant report

Variant	rs17616991
Chromosome Location	chr5:128303406-128303407
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 143 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs11241987	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743171	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1181983	0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs1181985	0.84[EUR][1000 genomes]
rs13166325	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13190393	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17616784	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17616974	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs17678874	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1898543	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1898544	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1898549	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2526196	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2526201	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2526202	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2526209	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2526210	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2526211	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2526212	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2526213	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2526214	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2526225	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2526239	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2526240	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2526241	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2526243	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2526245	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap]
rs2526246	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap]
rs2526247	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap]
rs2526248	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526249	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526252	1.00[CHB][hapmap]
rs2526253	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526255	0.80[CEU][hapmap]
rs2526257	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2545015	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2577399	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2577402	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2577403	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2577423	0.86[EUR][1000 genomes]
rs2577424	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs2577426	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577428	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577429	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577430	0.95[CEU][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577432	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577433	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577435	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577436	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577437	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577438	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577439	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577440	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577442	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577443	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577445	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577446	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577477	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2577504	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2577506	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2577507	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2577508	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2577509	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2577510	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2577511	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2577512	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2577513	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2577514	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2577528	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577529	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577530	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577533	1.00[CHB][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577534	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577535	0.82[CHB][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577536	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577537	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577538	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2577540	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap]
rs2577541	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.83[YRI][hapmap]
rs2577542	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577543	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577544	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577545	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577547	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577555	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2577556	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2577560	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2577561	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2577562	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3094874	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3098299	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3098300	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34075274	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34299037	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34683252	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34745544	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34813132	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34831887	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35044703	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35386300	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35388070	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35696888	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35767068	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35779465	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35869181	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36139771	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36149993	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36155285	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36157890	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36171961	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36175029	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36181441	0.80[ASN][1000 genomes]
rs36182790	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs36188905	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36190577	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs36191603	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36192190	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36192465	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62391271	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62391272	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62391297	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62399671	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62399674	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs62399676	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62399681	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62399682	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62399683	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62399685	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67198161	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861986	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881009	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881032	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71587998	0.83[AMR][1000 genomes]
rs71592877	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7349831	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882839	chr5:128205828-128390167	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv882840	chr5:128205828-128428962	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830485	chr5:128298622-128480492	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv882841	chr5:128301971-128400356	Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv882842	chr5:128301971-128552706	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17616991	CCNI2	cis	cerebellum	SCAN
rs17616991	SLC27A6	cis	parietal	SCAN
rs17616991	SLC27A6	cis	cerebellum	SCAN
rs17616991	SHROOM1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:128300600-128303600	Active TSS	Right Ventricle	heart
2	chr5:128303000-128308800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:128303000-128309000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:128303200-128312600	Weak transcription	Fetal Heart	heart
5	chr5:128303400-128319400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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