Variant report

Variant	rs1496530
Chromosome Location	chr8:86255898-86255899
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10090196	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs10095352	1.00[JPT][hapmap]
rs10097917	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1014303	0.89[ASN][1000 genomes]
rs1021583	0.82[JPT][hapmap]
rs1032551	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10504812	0.95[JPT][hapmap]
rs10504813	1.00[JPT][hapmap]
rs10907474	0.95[JPT][hapmap]
rs11261471	0.86[JPT][hapmap]
rs11261472	0.89[ASN][1000 genomes]
rs11261474	1.00[JPT][hapmap]
rs11985733	1.00[JPT][hapmap]
rs11989660	0.89[ASN][1000 genomes]
rs12114575	0.89[ASN][1000 genomes]
rs12541445	0.86[JPT][hapmap]
rs12543256	0.82[JPT][hapmap]
rs12544332	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12546106	0.82[JPT][hapmap]
rs12550160	0.82[JPT][hapmap]
rs1303806	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1303807	0.96[ASN][1000 genomes]
rs13252971	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs13259399	0.86[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs1390711	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1472360	0.83[ASN][1000 genomes]
rs1493302	1.00[JPT][hapmap]
rs1496526	0.84[ASN][1000 genomes]
rs1496529	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1496531	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];0.83[CHB][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1532423	0.95[JPT][hapmap]
rs1532424	1.00[JPT][hapmap]
rs1553015	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs16913681	0.82[JPT][hapmap]
rs16913721	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs17042	0.95[JPT][hapmap]
rs17740658	0.82[JPT][hapmap]
rs1995056	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs1995057	0.86[JPT][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap]
rs1995058	0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.95[ASN][1000 genomes]
rs2006767	0.91[CHD][hapmap];0.91[JPT][hapmap]
rs2055077	0.95[JPT][hapmap]
rs20571	1.00[JPT][hapmap]
rs2072696	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2132589	0.82[JPT][hapmap]
rs2220972	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2278459	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs2279701	0.86[JPT][hapmap]
rs2291786	0.82[JPT][hapmap]
rs2291787	0.86[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs2307075	1.00[JPT][hapmap]
rs2403104	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2453868	0.82[ASN][1000 genomes]
rs2548281	0.81[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2645047	0.83[ASN][1000 genomes]
rs2645049	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2645053	0.81[ASN][1000 genomes]
rs28494527	0.86[ASN][1000 genomes]
rs2896452	0.86[JPT][hapmap]
rs3087782	0.95[JPT][hapmap]
rs35285802	0.81[ASN][1000 genomes]
rs3758076	1.00[JPT][hapmap]
rs3758078	0.84[JPT][hapmap]
rs3779901	0.82[JPT][hapmap]
rs3808538	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs3808539	0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs4150868	0.81[JPT][hapmap]
rs4150942	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs4150964	0.82[JPT][hapmap]
rs4150974	0.82[JPT][hapmap]
rs4150977	0.82[JPT][hapmap]
rs4566	1.00[JPT][hapmap]
rs4609189	0.82[JPT][hapmap]
rs4739700	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs4739702	0.89[ASN][1000 genomes]
rs4740044	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs4740045	0.82[JPT][hapmap]
rs4740048	0.87[ASN][1000 genomes]
rs4740049	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs6605610	0.82[JPT][hapmap]
rs6605611	0.81[JPT][hapmap]
rs66498753	0.81[ASN][1000 genomes]
rs6988475	1.00[JPT][hapmap]
rs6990449	0.87[JPT][hapmap]
rs6993387	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs6994113	0.82[JPT][hapmap]
rs6997458	0.95[JPT][hapmap]
rs7001359	0.86[JPT][hapmap]
rs7004871	0.83[ASN][1000 genomes]
rs7008772	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs7011926	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7016369	0.95[JPT][hapmap]
rs725605	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs7818163	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs7827175	0.82[JPT][hapmap]
rs7833737	0.94[ASN][1000 genomes]
rs7835303	0.89[ASN][1000 genomes]
rs7837275	0.82[ASN][1000 genomes]
rs903895	0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.92[ASN][1000 genomes]
rs903896	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs903897	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs931505	0.95[JPT][hapmap]
rs9969643	1.00[JPT][hapmap]
rs9987281	1.00[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	esv3386656	chr8:86255600-86257598	Weak transcription Enhancers Bivalent Enhancer	TF binding region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1496530	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs1496530	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs1496530	CA2	cis	lymphoblastoid	seeQTL
rs1496530	C8orf59	cis	cerebellum	SCAN
rs1496530	C8orf59	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86244800-86263600	Weak transcription	Fetal Intestine Large	intestine
2	chr8:86253000-86257200	Weak transcription	Psoas Muscle	Psoas
3	chr8:86254600-86256400	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr8:86255000-86256200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr8:86255400-86256000	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr8:86255400-86257200	Weak transcription	HepG2	liver
7	chr8:86255800-86257200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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