Variant report

Variant	rs2406939
Chromosome Location	chr13:49220193-49220194
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49212874..49214823-chr13:49219265..49221630,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1009717	0.96[ASN][1000 genomes]
rs1009718	0.96[ASN][1000 genomes]
rs11840006	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12867213	0.97[ASN][1000 genomes]
rs12874937	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359108	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1359109	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1575920	0.96[ASN][1000 genomes]
rs1854017	0.96[ASN][1000 genomes]
rs2406937	0.96[ASN][1000 genomes]
rs2406938	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs35109670	0.86[ASN][1000 genomes]
rs4451857	0.96[ASN][1000 genomes]
rs6561469	0.96[ASN][1000 genomes]
rs6561471	0.85[ASN][1000 genomes]
rs6561474	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7324562	0.94[ASN][1000 genomes]
rs7332030	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7989287	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7990619	0.96[ASN][1000 genomes]
rs7990660	0.96[ASN][1000 genomes]
rs8000783	0.84[EUR][1000 genomes]
rs8001736	0.97[ASN][1000 genomes]
rs8002035	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9535059	0.82[ASN][1000 genomes]
rs9535060	0.97[ASN][1000 genomes]
rs9562833	0.96[ASN][1000 genomes]
rs9568056	0.96[ASN][1000 genomes]
rs9568058	0.96[ASN][1000 genomes]
rs9568059	0.81[ASN][1000 genomes]
rs9568061	0.95[ASN][1000 genomes]
rs9568062	0.96[ASN][1000 genomes]
rs9568064	0.97[ASN][1000 genomes]
rs9568065	0.97[ASN][1000 genomes]
rs9568069	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9591187	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9595943	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9595944	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9595945	0.83[ASN][1000 genomes]
rs9595950	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs964413	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv832605	chr13:49171305-49344970	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3495983	chr13:49181790-49222165	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3495984	chr13:49181790-49222165	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv525996	chr13:49210802-49222178	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2406939	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49215200-49221000	Weak transcription	Dnd41	blood
2	chr13:49217000-49221000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr13:49217600-49221000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr13:49218000-49220200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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