Variant report

Variant	rs1486113
Chromosome Location	chr1:72480789-72480790
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1016126	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10493489	0.82[TSI][hapmap]
rs10889934	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10889936	0.81[ASN][1000 genomes]
rs10889938	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12026691	0.82[TSI][hapmap]
rs1426173	0.87[CEU][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs1486089	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1486099	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1486100	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1486102	0.87[ASN][1000 genomes]
rs1812738	0.81[ASN][1000 genomes]
rs1843582	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1937185	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1937189	0.81[ASN][1000 genomes]
rs2052722	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2114214	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs2256783	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2422058	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2422059	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2489821	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2554417	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2630388	0.81[LWK][hapmap]
rs2630389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2630417	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2630418	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2768376	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2768378	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2768395	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2801322	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2801328	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2821282	0.81[LWK][hapmap]
rs3102902	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102905	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102906	0.89[LWK][hapmap]
rs3102908	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3102917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap]
rs3102923	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3128549	0.89[LWK][hapmap]
rs3128550	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3128557	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4111091	0.81[ASN][1000 genomes]
rs6424453	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6424454	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6666863	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap]
rs7511981	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7544722	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7544750	0.81[ASN][1000 genomes]
rs7550950	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv817447	chr1:72098815-72558020	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv916783	chr1:72196061-72707953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007910	chr1:72247302-72543998	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv428763	chr1:72353556-72499701	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1007073	chr1:72419858-72734657	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv546478	chr1:72442018-72512391	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv818223	chr1:72477221-72482645	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
8	nsv1006076	chr1:72477436-72700903	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv534996	chr1:72477436-72700903	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1486113	LRRIQ3	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72475800-72486400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:72476200-72488800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:72476400-72482400	Weak transcription	Left Ventricle	heart

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