Variant report

Variant	rs2280404
Chromosome Location	chr2:30945896-30945897
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1057511	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13388696	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13414988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593430	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2593433	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2593447	0.83[EUR][1000 genomes]
rs2609911	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2681682	0.88[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2681683	0.88[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2681684	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34079417	0.93[ASN][1000 genomes]
rs6548029	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6711743	0.89[ASN][1000 genomes]
rs6735522	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6748488	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs751062	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9309682	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9309683	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9309684	0.84[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9309685	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9679326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9679386	0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription 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	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2280404	MRPL33	cis	cerebellum	SCAN
rs2280404	KHK	cis	cerebellum	SCAN
rs2280404	CENPA	cis	cerebellum	SCAN
rs2280404	LCLAT1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30902400-30954000	Weak transcription	Gastric	stomach
2	chr2:30938400-30946000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:30940600-30969600	Weak transcription	Stomach Mucosa	stomach
4	chr2:30943000-30951400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:30945800-30955400	Weak transcription	Fetal Intestine Small	intestine

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