Variant report

Variant	rs2593430
Chromosome Location	chr2:30951984-30951985
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1057511	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13388696	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13414988	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13428030	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2276567	0.86[CHB][hapmap]
rs2280404	0.84[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2593433	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2593437	0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs2609911	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2681682	0.81[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2681683	0.81[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2681684	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6548029	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6735522	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6748488	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs751062	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9309682	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9309683	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9309684	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9309685	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9679326	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][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
rs2593430	KHK	cis	cerebellum	SCAN
rs2593430	CENPA	cis	cerebellum	SCAN
rs2593430	MRPL33	cis	cerebellum	SCAN
rs2593430	PPP1CB	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30902400-30954000	Weak transcription	Gastric	stomach
2	chr2:30940600-30969600	Weak transcription	Stomach Mucosa	stomach
3	chr2:30945800-30955400	Weak transcription	Fetal Intestine Small	intestine
4	chr2:30946800-30953200	Weak transcription	Fetal Stomach	stomach
5	chr2:30947400-30953000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr2:30950000-30954200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr2:30951400-30954000	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr2:30951800-30952400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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