Variant report

Variant	rs4740049
Chromosome Location	chr8:86250709-86250710
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10088120	0.82[JPT][hapmap];0.88[MEX][hapmap]
rs10090196	0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap]
rs10095352	0.95[JPT][hapmap]
rs10107686	0.81[ASN][1000 genomes]
rs1014303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1021583	0.86[JPT][hapmap]
rs10504812	0.91[JPT][hapmap]
rs10504813	0.95[JPT][hapmap]
rs10907474	0.91[JPT][hapmap]
rs11261471	0.91[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs11261472	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11261474	0.95[JPT][hapmap]
rs11985733	0.95[JPT][hapmap]
rs11989660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12114575	0.92[ASN][1000 genomes]
rs12541445	0.91[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs12543256	0.86[JPT][hapmap]
rs12544332	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12546106	0.86[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs12550160	0.86[JPT][hapmap]
rs1303806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1303807	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13252971	0.95[JPT][hapmap]
rs13259399	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13269739	0.82[JPT][hapmap]
rs1390711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1493302	0.95[JPT][hapmap]
rs1496526	0.81[ASN][1000 genomes]
rs1496529	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1496530	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1496531	0.86[JPT][hapmap]
rs1496532	0.86[JPT][hapmap]
rs1532423	0.91[JPT][hapmap]
rs1532424	0.95[JPT][hapmap]
rs1553015	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];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16913681	0.86[JPT][hapmap]
rs16913721	0.91[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs17042	0.91[JPT][hapmap]
rs17740658	0.86[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs1908762	0.82[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs1995056	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1995057	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs1995058	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2006767	0.91[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs2055077	0.91[JPT][hapmap]
rs20571	0.95[JPT][hapmap]
rs2072696	0.95[JPT][hapmap]
rs2132589	0.86[JPT][hapmap];0.83[TSI][hapmap]
rs2278459	0.83[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs2279701	0.91[JPT][hapmap]
rs2291786	0.86[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs2291787	0.83[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2307075	0.95[JPT][hapmap]
rs2403083	0.82[JPT][hapmap]
rs2403085	0.82[JPT][hapmap]
rs2403086	0.82[JPT][hapmap]
rs2403104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2548281	0.91[JPT][hapmap]
rs2645047	0.81[ASN][1000 genomes]
rs2645049	0.81[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs28494527	0.90[ASN][1000 genomes]
rs2896452	0.91[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs2896454	0.82[JPT][hapmap];0.88[MEX][hapmap]
rs3087782	0.91[JPT][hapmap]
rs35285802	0.85[ASN][1000 genomes]
rs3758076	0.95[JPT][hapmap]
rs3779899	0.81[JPT][hapmap];0.92[MEX][hapmap]
rs3779901	0.86[JPT][hapmap]
rs3808538	0.86[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3808539	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3808540	0.91[CEU][hapmap];0.82[GIH][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4150867	0.82[JPT][hapmap]
rs4150868	0.81[JPT][hapmap]
rs4150869	0.80[JPT][hapmap]
rs4150893	0.82[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap]
rs4150909	0.82[JPT][hapmap]
rs4150942	0.83[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap]
rs4150944	0.82[JPT][hapmap]
rs4150964	0.86[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs4150974	0.86[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs4150977	0.86[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs4566	0.95[JPT][hapmap]
rs4609189	0.86[JPT][hapmap]
rs4739700	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4739702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4740044	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4740045	0.86[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs4740048	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62527225	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6605610	0.86[JPT][hapmap]
rs6605611	0.86[JPT][hapmap]
rs67573812	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6987641	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6988475	0.95[JPT][hapmap]
rs6990449	0.82[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6990452	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6993387	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6994113	0.86[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs6997458	0.91[JPT][hapmap]
rs7001359	0.91[JPT][hapmap]
rs7004871	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7008772	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7011926	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7015758	0.82[JPT][hapmap]
rs7016369	0.91[JPT][hapmap]
rs725605	0.86[JPT][hapmap]
rs7818163	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7827175	0.86[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs7829050	0.82[JPT][hapmap]
rs7833737	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7835303	0.92[ASN][1000 genomes]
rs7835882	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7837275	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs903895	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs903896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs903897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs931505	0.91[JPT][hapmap]
rs9969643	0.95[JPT][hapmap]
rs9987281	0.95[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4740049	LRRCC1	cis	cerebellum	SCAN
rs4740049	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs4740049	C8orf59	cis	parietal	SCAN
rs4740049	C8orf59	cis	cerebellum	SCAN
rs4740049	CA13	cis	lymphoblastoid	seeQTL
rs4740049	LRRCC1	cis	Esophagus Mucosa	GTEx
rs4740049	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 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	chr8:86249200-86251600	Weak transcription	Rectal Mucosa Donor 31	rectum

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