Variant report

Variant	rs12420220
Chromosome Location	chr11:57714598-57714599
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr11:57713963-57714642	GM12878	blood:	n/a	chr11:57714307-57714316 chr11:57714304-57714317 chr11:57714305-57714318 chr11:57714311-57714320 chr11:57714308-57714315

Variant related genes	Relation type
OR5BD1P	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10792118	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1113095	0.80[EUR][1000 genomes]
rs11229170	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11229171	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229172	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11229173	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229183	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11512731	0.87[ASN][1000 genomes]
rs11512732	0.84[ASN][1000 genomes]
rs12366063	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1510418	0.82[EUR][1000 genomes]
rs1848879	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34419144	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35241049	0.82[EUR][1000 genomes]
rs35994197	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4245215	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4272798	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs588713	0.89[EUR][1000 genomes]
rs591322	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs593239	0.83[EUR][1000 genomes]
rs600488	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs602861	0.86[EUR][1000 genomes]
rs606731	0.86[EUR][1000 genomes]
rs615133	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs616911	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61905278	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs626043	0.82[EUR][1000 genomes]
rs633129	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs636388	0.83[EUR][1000 genomes]
rs652191	0.80[YRI][hapmap]
rs6591443	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662638	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs681397	0.88[EUR][1000 genomes]
rs7103977	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7106195	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7119973	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71484480	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7926999	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7943793	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv983185	chr11:57714356-57732279	Enhancers Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12420220	YPEL4	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57713800-57714800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr11:57713800-57720600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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