Variant report

Variant	rs13016064
Chromosome Location	chr2:145458485-145458486
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:145453934..145456976-chr2:145457587..145463055,5	K562	blood:
2	chr2:145383800..145385697-chr2:145457704..145459844,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARHGAP15-16	chr2:145456944-145465439	NONHSAT074810

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10200647	0.98[ASN][1000 genomes]
rs10203655	0.98[ASN][1000 genomes]
rs10205995	0.87[ASN][1000 genomes]
rs10432351	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10496966	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10803510	0.83[JPT][hapmap]
rs10928224	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10928225	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10928226	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10928227	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11674690	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11679253	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11883829	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap]
rs11900456	0.96[ASN][1000 genomes]
rs11902294	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs12104619	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12471698	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12478142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12611966	0.88[ASN][1000 genomes]
rs12623452	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs12991932	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12997597	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13003467	0.98[ASN][1000 genomes]
rs13008442	0.88[ASN][1000 genomes]
rs13015001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13032840	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13413613	0.87[ASN][1000 genomes]
rs1346344	0.83[JPT][hapmap]
rs1351734	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1365902	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1365905	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1384779	0.88[ASN][1000 genomes]
rs1384783	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1427500	0.83[JPT][hapmap]
rs1427507	0.83[JPT][hapmap]
rs1427509	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];1.00[ASN][1000 genomes]
rs1483491	0.96[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1483499	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1529386	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1529387	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1559961	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1559962	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1564697	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1896453	0.93[ASN][1000 genomes]
rs1896454	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1905347	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1994155	0.88[ASN][1000 genomes]
rs2086748	0.89[ASN][1000 genomes]
rs2162571	0.83[JPT][hapmap]
rs2195114	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2195115	0.94[ASN][1000 genomes]
rs2254435	0.99[ASN][1000 genomes]
rs2381651	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]
rs35099259	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs3856364	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4271712	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4458150	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4471836	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4662231	0.87[ASN][1000 genomes]
rs4662232	0.96[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4662393	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61440197	0.90[ASN][1000 genomes]
rs6707047	0.97[ASN][1000 genomes]
rs6728198	0.97[ASN][1000 genomes]
rs6745079	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72991962	0.90[ASN][1000 genomes]
rs7575857	0.87[ASN][1000 genomes]
rs7579453	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580571	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs900554	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs958500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs958501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs980772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs990847	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[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	nsv1002563	chr2:145182201-145863253	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv535957	chr2:145182201-145863253	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv529501	chr2:145257682-145485605	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv834397	chr2:145439528-145608628	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13016064	RNF34	trans	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:145450400-145469200	Weak transcription	Aorta	Aorta
2	chr2:145457200-145464600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr2:145457400-145459800	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr2:145457600-145458600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr2:145457800-145463600	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr2:145458400-145459800	Enhancers	Primary B cells from cord blood	blood

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