Variant report

Variant	rs1553016
Chromosome Location	chr8:86218398-86218399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 151 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10088120	0.91[JPT][hapmap]
rs10090196	0.86[JPT][hapmap]
rs10091582	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10095352	0.86[JPT][hapmap]
rs10097917	0.84[ASN][1000 genomes]
rs10099251	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10100442	0.84[JPT][hapmap]
rs10106970	0.82[ASN][1000 genomes]
rs10107686	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10110461	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10111971	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1014303	0.82[ASN][1000 genomes]
rs1021583	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10504812	0.82[JPT][hapmap]
rs10504813	0.86[JPT][hapmap]
rs10907474	0.82[JPT][hapmap]
rs11261468	0.81[JPT][hapmap]
rs11261469	0.90[ASN][1000 genomes]
rs11261471	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11261472	0.82[ASN][1000 genomes]
rs11261474	0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs11985733	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs11989660	0.82[ASN][1000 genomes]
rs12114575	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12541299	0.99[ASN][1000 genomes]
rs12541445	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12543256	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12544332	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12546106	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12550160	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12679400	0.84[ASN][1000 genomes]
rs1303806	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs13252971	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs13259399	0.86[JPT][hapmap]
rs13269739	0.90[JPT][hapmap];0.82[TSI][hapmap]
rs1390711	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs1493302	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1496529	0.86[JPT][hapmap]
rs1496530	0.86[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs1496531	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs1496532	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs1496533	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1532423	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1532424	0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs1553015	0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1553017	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16913681	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs16913721	0.86[JPT][hapmap]
rs17042	0.82[JPT][hapmap]
rs17740658	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1809819	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1845891	0.91[ASN][1000 genomes]
rs1845892	0.88[ASN][1000 genomes]
rs1908762	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs1995056	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs1995057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1995058	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2006767	0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2055077	0.82[JPT][hapmap]
rs20571	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2072696	0.85[JPT][hapmap]
rs2132589	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2132590	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2220972	0.88[ASN][1000 genomes]
rs2278459	0.81[JPT][hapmap]
rs2279700	0.96[ASN][1000 genomes]
rs2279701	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2291786	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2291787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2307075	0.86[JPT][hapmap]
rs2403083	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2403085	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs2403086	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2403088	0.81[JPT][hapmap]
rs2403104	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2548281	0.82[JPT][hapmap]
rs2645049	0.82[JPT][hapmap]
rs28374336	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28439950	0.88[ASN][1000 genomes]
rs28564613	0.84[ASN][1000 genomes]
rs2896452	0.81[JPT][hapmap]
rs2896454	0.91[JPT][hapmap]
rs3087782	0.82[JPT][hapmap]
rs34103685	0.91[JPT][hapmap]
rs35558766	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3758076	0.86[JPT][hapmap]
rs3779899	0.90[JPT][hapmap]
rs3779901	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3808538	0.86[JPT][hapmap]
rs3808539	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs4150867	0.91[JPT][hapmap]
rs4150868	0.90[JPT][hapmap]
rs4150869	0.85[JPT][hapmap]
rs4150893	0.83[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs4150909	0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs4150942	0.81[JPT][hapmap]
rs4150944	0.91[JPT][hapmap]
rs4150962	0.81[ASN][1000 genomes]
rs4150964	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4150974	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4150977	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4566	0.82[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs4609189	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4617148	0.91[ASN][1000 genomes]
rs4739698	0.88[ASN][1000 genomes]
rs4739700	0.86[JPT][hapmap]
rs4739702	0.82[ASN][1000 genomes]
rs4740044	0.86[JPT][hapmap]
rs4740045	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4740047	0.91[ASN][1000 genomes]
rs4740048	0.83[ASN][1000 genomes]
rs4740049	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs6605610	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6605611	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6605613	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6605624	0.80[JPT][hapmap]
rs6988475	0.86[JPT][hapmap]
rs6990449	0.86[JPT][hapmap]
rs6993316	0.91[ASN][1000 genomes]
rs6993387	0.86[JPT][hapmap]
rs6994113	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6997458	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7001359	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7008772	0.86[JPT][hapmap]
rs7011001	0.84[ASN][1000 genomes]
rs7011926	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs7015758	0.91[JPT][hapmap]
rs7016369	0.82[JPT][hapmap]
rs725605	0.86[CHB][hapmap]
rs7818163	0.86[JPT][hapmap]
rs7821629	0.83[ASN][1000 genomes]
rs7826511	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7827175	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7829050	0.91[JPT][hapmap]
rs7829144	0.81[JPT][hapmap]
rs7829240	0.82[ASN][1000 genomes]
rs7835303	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7839129	0.90[ASN][1000 genomes]
rs7841142	0.81[JPT][hapmap]
rs903895	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs903896	0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs903897	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs931505	0.82[JPT][hapmap]
rs9329908	0.92[ASN][1000 genomes]
rs9969643	0.82[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs9987281	0.82[CHB][hapmap];0.86[JPT][hapmap]

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	nsv1018483	chr8:86142258-86547831	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024759	chr8:86162507-86361533	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv539659	chr8:86162507-86361533	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv971674	chr8:86187966-86338484	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	esv2761442	chr8:86201657-86230641	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1553016	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs1553016	C8orf59	cis	cerebellum	SCAN
rs1553016	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs1553016	CA13	cis	multi-tissue	Pritchard
rs1553016	C8orf59	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86197400-86225800	Weak transcription	Fetal Intestine Small	intestine
2	chr8:86211600-86222000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr8:86217400-86221600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr8:86217600-86229200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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