Variant report

Variant	rs292949
Chromosome Location	chr5:58038431-58038432
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	chr5:57946400..57947922-chr5:58037144..58039712,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1035393	0.97[EUR][1000 genomes]
rs1422226	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs149351	0.84[EUR][1000 genomes]
rs149525	0.88[EUR][1000 genomes]
rs158958	0.82[CEU][hapmap];0.85[CHB][hapmap]
rs158980	0.88[CEU][hapmap];0.89[TSI][hapmap]
rs158987	0.89[EUR][1000 genomes]
rs158993	0.81[CEU][hapmap]
rs158999	0.80[CEU][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs159000	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs159002	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs159003	0.80[EUR][1000 genomes]
rs159004	0.91[CEU][hapmap];0.85[CHB][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs159006	0.81[EUR][1000 genomes]
rs159007	0.91[CEU][hapmap];0.85[CHB][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs172397	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs172398	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs176637	0.89[EUR][1000 genomes]
rs176807	1.00[CEU][hapmap];0.81[CHB][hapmap];0.99[EUR][1000 genomes]
rs182391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs186010	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs1895232	1.00[CEU][hapmap];0.81[CHB][hapmap];0.99[EUR][1000 genomes]
rs2545789	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2591920	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2591922	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs290572	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs292948	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs293000	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs293002	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293005	1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs293006	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs293007	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs293008	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs293009	0.88[CEU][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs293010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs293013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs293014	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs293018	1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs293019	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs293025	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs293026	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[EUR][1000 genomes]
rs293027	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs293029	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs49961	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1029145	chr5:57905821-58141221	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830311	chr5:57912546-58105636	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs292949	MAP3K1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58027800-58049400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:58031800-58041400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:58036000-58040600	Weak transcription	Fetal Intestine Small	intestine
4	chr5:58036000-58040800	Weak transcription	Fetal Intestine Large	intestine
5	chr5:58038000-58039000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr5:58038000-58039000	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr5:58038200-58039000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr5:58038200-58039000	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr5:58038400-58038800	Enhancers	Fetal Brain Female	brain

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