Variant report

Variant	rs1541359
Chromosome Location	chr7:27456332-27456333
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	chr7:27455758..27458549-chr7:27459040..27460885,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10241677	1.00[JPT][hapmap]
rs10276966	1.00[JPT][hapmap]
rs11563953	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769034	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11981761	0.89[ASW][hapmap]
rs12700804	0.89[EUR][1000 genomes]
rs12700806	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1554637	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17429761	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28361582	0.86[YRI][hapmap]
rs34924985	0.92[EUR][1000 genomes]
rs34989520	0.92[EUR][1000 genomes]
rs35240477	0.91[EUR][1000 genomes]
rs35468459	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35713538	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915087	0.91[EUR][1000 genomes]
rs3915088	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722704	0.91[EUR][1000 genomes]
rs6957243	1.00[JPT][hapmap]
rs6958811	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958873	0.83[ASN][1000 genomes]
rs6970308	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979081	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71539516	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7784592	0.89[ASW][hapmap];0.93[CEU][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs969410	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531024	chr7:27194426-27461954	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
2	nsv830930	chr7:27395838-27587355	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1541359	HOXA3	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27444800-27458000	Weak transcription	Pancreas	Pancrea
2	chr7:27444800-27458000	Weak transcription	Stomach Mucosa	stomach

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