Variant report

Variant	rs1496531
Chromosome Location	chr8:86254062-86254063
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10090196	0.81[JPT][hapmap]
rs10091582	0.90[ASN][1000 genomes]
rs10095352	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs10097917	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10099251	0.90[ASN][1000 genomes]
rs10107686	0.95[ASN][1000 genomes]
rs10110461	0.89[ASN][1000 genomes]
rs10111971	0.90[ASN][1000 genomes]
rs1021583	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1032551	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10504812	0.86[JPT][hapmap]
rs10504813	0.91[JPT][hapmap]
rs10907474	0.86[JPT][hapmap]
rs11261471	0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11261474	0.95[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs11985733	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs12541299	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12541445	0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12543256	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs12544332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12546106	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs12550160	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs12550814	0.83[ASN][1000 genomes]
rs1303806	0.86[JPT][hapmap]
rs13252971	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs13259399	0.81[JPT][hapmap]
rs13269739	0.86[JPT][hapmap]
rs1390711	0.86[JPT][hapmap]
rs1390712	0.83[ASN][1000 genomes]
rs1493302	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1496529	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs1496530	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1496532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496533	0.94[ASN][1000 genomes]
rs1532423	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1532424	0.95[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs1553015	0.86[JPT][hapmap]
rs1553016	0.90[ASN][1000 genomes]
rs1553017	0.89[ASN][1000 genomes]
rs16913681	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs16913721	0.81[JPT][hapmap]
rs17042	0.86[JPT][hapmap]
rs17740658	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs1809819	0.91[ASN][1000 genomes]
rs1845891	0.81[ASN][1000 genomes]
rs1908762	0.86[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1995056	0.80[JPT][hapmap]
rs1995057	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.93[ASN][1000 genomes]
rs1995058	0.86[JPT][hapmap];0.85[TSI][hapmap]
rs2006767	0.82[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs2055077	0.86[JPT][hapmap]
rs20571	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2072696	0.90[JPT][hapmap]
rs2132589	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs2132590	0.82[ASN][1000 genomes]
rs2173044	0.83[ASN][1000 genomes]
rs2220972	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279700	0.86[ASN][1000 genomes]
rs2279701	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2291786	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs2291787	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.95[ASN][1000 genomes]
rs2307075	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs2403083	0.86[JPT][hapmap]
rs2403085	0.86[JPT][hapmap]
rs2403086	0.86[JPT][hapmap]
rs2403104	0.85[JPT][hapmap]
rs2548281	0.86[JPT][hapmap]
rs2645049	0.86[JPT][hapmap]
rs28374336	0.90[ASN][1000 genomes]
rs2896454	0.86[JPT][hapmap]
rs3087782	0.86[JPT][hapmap]
rs35558766	0.89[ASN][1000 genomes]
rs3758076	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs3779899	0.86[JPT][hapmap]
rs3779901	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs3808538	0.81[JPT][hapmap]
rs3808539	0.86[JPT][hapmap];0.82[TSI][hapmap]
rs4150867	0.86[JPT][hapmap]
rs4150868	0.90[JPT][hapmap]
rs4150869	0.80[JPT][hapmap]
rs4150893	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs4150909	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs4150944	0.86[JPT][hapmap]
rs4150964	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs4150974	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs4150977	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs4566	0.86[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs4609189	0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4617148	0.81[ASN][1000 genomes]
rs4739700	0.81[JPT][hapmap]
rs4740044	0.81[JPT][hapmap]
rs4740045	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs4740047	0.81[ASN][1000 genomes]
rs4740049	0.86[JPT][hapmap]
rs6605610	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs6605611	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs6605613	0.89[ASN][1000 genomes]
rs6988475	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs6993316	0.81[ASN][1000 genomes]
rs6993387	0.81[JPT][hapmap]
rs6994113	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs6997458	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7001359	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7008772	0.81[JPT][hapmap]
rs7011926	0.86[JPT][hapmap]
rs7015758	0.86[JPT][hapmap]
rs7016369	0.86[JPT][hapmap]
rs725605	0.83[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs7818163	0.81[JPT][hapmap]
rs7824715	0.84[ASN][1000 genomes]
rs7826511	0.93[ASN][1000 genomes]
rs7827175	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs903895	0.86[JPT][hapmap];0.85[TSI][hapmap]
rs903896	0.86[JPT][hapmap]
rs903897	0.86[JPT][hapmap]
rs931505	0.86[JPT][hapmap]
rs9329908	0.82[ASN][1000 genomes]
rs9969643	0.86[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs9987281	0.86[CHB][hapmap];0.91[JPT][hapmap]

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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1496531	LRRCC1	cis	Esophagus Mucosa	GTEx
rs1496531	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs1496531	C8orf59	cis	cerebellum	SCAN
rs1496531	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs1496531	C8orf59	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86238800-86254800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr8:86244800-86263600	Weak transcription	Fetal Intestine Large	intestine
3	chr8:86253000-86257200	Weak transcription	Psoas Muscle	Psoas
4	chr8:86254000-86254600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr8:86254000-86255400	Weak transcription	Rectal Mucosa Donor 29	rectum

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