Variant report

Variant	rs173580
Chromosome Location	chr5:127020565-127020566
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:127018619..127020930-chr5:127030994..127033647,2	K562	blood:

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10041967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10061252	0.94[EUR][1000 genomes]
rs1007623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10519953	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1086523	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1086524	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1086525	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1086526	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1086527	0.96[EUR][1000 genomes]
rs1086529	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1086530	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1086531	0.96[EUR][1000 genomes]
rs1086532	0.96[EUR][1000 genomes]
rs1086533	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1086534	0.93[EUR][1000 genomes]
rs1088167	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900792	0.96[EUR][1000 genomes]
rs1092720	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11241938	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11241939	0.94[EUR][1000 genomes]
rs11950864	0.95[CEU][hapmap]
rs1213827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1228156	0.82[EUR][1000 genomes]
rs1234542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12652197	0.96[EUR][1000 genomes]
rs12653785	0.81[EUR][1000 genomes]
rs1432958	0.96[EUR][1000 genomes]
rs1515640	0.83[EUR][1000 genomes]
rs1560673	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs173581	0.95[EUR][1000 genomes]
rs173582	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1816404	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1816405	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs187461	0.95[EUR][1000 genomes]
rs1897525	0.82[EUR][1000 genomes]
rs193736	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs248689	1.00[CEU][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs248690	0.91[EUR][1000 genomes]
rs248691	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs248692	1.00[CEU][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs248696	0.92[EUR][1000 genomes]
rs248698	0.92[EUR][1000 genomes]
rs248700	0.90[EUR][1000 genomes]
rs248701	0.91[EUR][1000 genomes]
rs248702	0.91[EUR][1000 genomes]
rs248706	0.91[EUR][1000 genomes]
rs248709	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs248711	0.96[EUR][1000 genomes]
rs248712	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248713	0.96[EUR][1000 genomes]
rs248715	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248716	0.97[EUR][1000 genomes]
rs248717	0.95[EUR][1000 genomes]
rs248718	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248720	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs248721	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs248722	0.97[EUR][1000 genomes]
rs248724	1.00[CEU][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs248730	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs248731	0.96[EUR][1000 genomes]
rs248732	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs248733	0.96[EUR][1000 genomes]
rs248735	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs248737	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs248738	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs248739	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs248740	0.96[EUR][1000 genomes]
rs248741	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs248742	0.96[EUR][1000 genomes]
rs2569142	0.96[EUR][1000 genomes]
rs2569144	0.96[EUR][1000 genomes]
rs2569146	0.82[EUR][1000 genomes]
rs2673749	0.95[EUR][1000 genomes]
rs2673750	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2673763	0.95[EUR][1000 genomes]
rs2673764	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2673772	1.00[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs4340958	0.91[EUR][1000 genomes]
rs4361571	0.94[EUR][1000 genomes]
rs45074	0.91[EUR][1000 genomes]
rs54201	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59513079	0.82[EUR][1000 genomes]
rs62373501	0.96[EUR][1000 genomes]
rs62373502	0.95[EUR][1000 genomes]
rs6595789	0.97[EUR][1000 genomes]
rs7714847	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7736233	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs790827	0.89[EUR][1000 genomes]
rs791071	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs791072	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs791073	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs791074	0.96[EUR][1000 genomes]
rs809349	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs812059	0.87[EUR][1000 genomes]
rs899190	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv830479	chr5:126849254-127053121	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv830480	chr5:126964751-127124522	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs173580	LYRM7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127002800-127022200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:127016600-127021000	Weak transcription	Hela-S3	cervix
3	chr5:127019000-127022200	Weak transcription	Ovary	ovary
4	chr5:127019800-127020600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:127019800-127021000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr5:127019800-127022200	Weak transcription	Psoas Muscle	Psoas
7	chr5:127020400-127023000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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