Variant report

Variant	rs2526243
Chromosome Location	chr5:128300176-128300177
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr5:128300150-128301590	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:128299750..128303179-chr5:128428591..128431385,3	MCF-7	breast:

Variant related genes	Relation type
SLC27A6	TF binding region
ENSG00000066583	Chromatin interaction

Extended variants
information (count: 144 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs11241987	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11740215	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11743171	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1181983	0.86[TSI][hapmap]
rs12189398	0.83[ASN][1000 genomes]
rs12518184	0.83[ASN][1000 genomes]
rs13166325	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13169590	0.86[ASN][1000 genomes]
rs13190393	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421890	0.94[ASN][1000 genomes]
rs17616784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17616974	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]
rs17616991	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]
rs17678874	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1898543	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1898544	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1898549	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2522383	0.84[CEU][hapmap]
rs2526196	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526201	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526202	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526209	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526210	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526211	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526212	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526213	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526214	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526225	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2526239	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2526240	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526245	0.93[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2526246	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs2526247	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2526248	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2526249	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2526251	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2526252	1.00[CHB][hapmap]
rs2526253	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2526257	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2545015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2577399	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577402	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577403	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577423	0.80[EUR][1000 genomes]
rs2577424	0.80[CEU][hapmap]
rs2577426	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2577428	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2577429	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2577430	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2577432	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2577433	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2577435	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2577436	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2577437	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2577438	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2577439	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2577440	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2577442	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2577443	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2577445	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577446	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577477	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2577489	0.84[CEU][hapmap]
rs2577504	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577506	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577507	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577508	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577509	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577510	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577511	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577512	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577513	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577514	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577528	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577529	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577530	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577533	0.86[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577535	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577536	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577537	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577538	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577539	0.88[JPT][hapmap]
rs2577540	0.93[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2577541	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[YRI][hapmap];0.92[ASN][1000 genomes]
rs2577542	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577543	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577544	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577545	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577546	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577547	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577555	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577556	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577560	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577561	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577562	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094874	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3098299	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3098300	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34075274	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34299037	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34683252	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34813132	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34831887	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35044703	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35386300	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35388070	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35590597	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35696888	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35767068	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35779465	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35869181	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36139771	0.87[AMR][1000 genomes]
rs36147677	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs36149993	0.85[AMR][1000 genomes]
rs36155285	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36157890	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36171961	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36175029	0.85[AMR][1000 genomes]
rs36188905	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36191603	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36192190	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36192465	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62391271	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62391272	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62391297	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62399671	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62399676	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62399681	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62399682	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62399683	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62399685	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67198161	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6861986	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6881009	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6881032	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71587998	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71587999	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs71592877	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7349831	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2526243	SLC27A6	cis	parietal	SCAN
rs2526243	PITPNC1	trans	lymphoblastoid	seeQTL
rs2526243	CCNI2	cis	cerebellum	SCAN
rs2526243	SLC27A6	cis	cerebellum	SCAN
rs2526243	SHROOM1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:128300000-128300400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr5:128300000-128300400	Enhancers	Fetal Heart	heart

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