Variant report

Variant	rs9526819
Chromosome Location	chr13:52563475-52563476
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52555699..52557383-chr13:52562997..52565551,2	MCF-7	breast:
2	chr13:52561953..52567975-chr13:52568159..52572243,8	K562	blood:
3	chr13:52562562..52567113-chr13:52569338..52572980,4	MCF-7	breast:

Extended variants
information (count: 130 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1004576	0.87[CHB][hapmap]
rs1055062	0.87[CHB][hapmap]
rs1060631	0.87[CHB][hapmap]
rs11616964	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11620583	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12146904	0.86[CHB][hapmap]
rs12431310	0.86[CHB][hapmap]
rs1571189	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs1801243	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1801244	0.85[CEU][hapmap];0.87[MEX][hapmap];0.90[AMR][1000 genomes]
rs1886538	0.95[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1886542	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.80[YRI][hapmap]
rs1886543	0.87[CHB][hapmap]
rs1886544	0.87[CHB][hapmap]
rs1886547	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs1924611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951922	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1998696	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2004866	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2147359	0.80[ASN][1000 genomes]
rs2147360	0.80[ASN][1000 genomes]
rs2181891	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2274202	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs2277448	0.87[CHB][hapmap]
rs2296347	0.87[CHB][hapmap]
rs2296348	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs2296349	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs2408544	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2408549	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2408550	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2408551	0.93[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2408552	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs2408554	0.87[CHB][hapmap]
rs2408609	0.86[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs2408611	0.86[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap]
rs2897964	0.86[CHB][hapmap]
rs2897977	0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs3368	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap]
rs35895576	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3742288	0.85[CEU][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.90[AMR][1000 genomes]
rs3742289	0.87[CHB][hapmap]
rs3783241	0.80[AMR][1000 genomes]
rs3783242	0.87[CHB][hapmap]
rs3818422	0.87[CHB][hapmap]
rs3825527	0.85[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.90[AMR][1000 genomes]
rs3825528	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4297592	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4497567	0.87[CHB][hapmap]
rs4600369	0.80[ASN][1000 genomes]
rs4941720	0.80[ASN][1000 genomes]
rs4941727	0.87[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap]
rs61958812	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6561656	0.87[CHB][hapmap]
rs723102	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs723103	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs732071	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7320831	0.87[CHB][hapmap]
rs7321120	0.87[CHB][hapmap]
rs7321435	0.95[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7321775	0.81[ASN][1000 genomes]
rs7324458	0.87[CHB][hapmap]
rs7327634	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7332272	0.84[ASN][1000 genomes]
rs7337430	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs747781	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs750290	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs755363	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap]
rs7981904	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs7991237	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap]
rs7993492	0.85[ASN][1000 genomes]
rs7994928	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7995946	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.80[EUR][1000 genomes]
rs7998770	0.87[CHB][hapmap]
rs7999812	0.84[CEU][hapmap];0.90[AMR][1000 genomes]
rs9316563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526817	0.80[ASN][1000 genomes]
rs9526821	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526823	0.87[CHB][hapmap]
rs9526825	0.87[CHB][hapmap]
rs9526832	0.81[EUR][1000 genomes]
rs9526837	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap]
rs9526841	0.87[CHB][hapmap]
rs9526842	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9535812	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535813	0.80[ASN][1000 genomes]
rs9535816	0.81[ASN][1000 genomes]
rs9535817	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535819	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535822	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535823	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535824	0.81[ASN][1000 genomes]
rs9535825	0.95[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs9535826	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535828	0.87[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535829	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535830	0.83[ASN][1000 genomes]
rs9535832	0.82[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9535833	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535836	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535851	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9535856	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap]
rs9535858	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap]
rs9535860	0.81[EUR][1000 genomes]
rs9535862	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.80[EUR][1000 genomes]
rs9535866	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.80[EUR][1000 genomes]
rs9535867	0.87[CHB][hapmap]
rs9535873	0.87[CHB][hapmap]
rs9535878	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.80[YRI][hapmap]
rs9535879	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs9535880	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs9535882	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap]
rs9535885	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9535887	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.80[YRI][hapmap]
rs9563084	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9563089	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9568681	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9568682	0.95[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9568684	0.81[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs9568693	0.81[EUR][1000 genomes]
rs9568695	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9568713	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv455888	chr13:52491193-52570728	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv561649	chr13:52491193-52570728	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1041996	chr13:52544805-52581501	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
8	esv2763022	chr13:52544978-52581513	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
9	nsv900082	chr13:52555288-52709938	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9526819	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs9526819	CKAP2	cis	parietal	SCAN
rs9526819	CKAP2	cis	cerebellum	SCAN
rs9526819	NEK3	cis	cerebellum	SCAN
rs9526819	NCRNA00282	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52553400-52569400	Weak transcription	Pancreas	Pancrea
2	chr13:52555600-52568800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr13:52555800-52569200	Weak transcription	Left Ventricle	heart
4	chr13:52555800-52570200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr13:52558000-52565000	Weak transcription	Fetal Intestine Small	intestine
6	chr13:52562200-52569400	Weak transcription	Fetal Intestine Large	intestine
7	chr13:52563400-52563600	Enhancers	Stomach Mucosa	stomach
8	chr13:52563400-52564000	Enhancers	Liver	Liver
9	chr13:52563400-52564600	Enhancers	HepG2	liver
10	chr13:52563400-52569200	Weak transcription	Duodenum Mucosa	Duodenum

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