Variant report

Variant	rs6518698
Chromosome Location	chr22:30921371-30921372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1001409	0.84[EUR][1000 genomes]
rs11912737	0.99[EUR][1000 genomes]
rs12165604	0.84[EUR][1000 genomes]
rs13053759	0.87[EUR][1000 genomes]
rs13054004	0.83[EUR][1000 genomes]
rs13750	0.86[CEU][hapmap];0.83[TSI][hapmap]
rs16988720	0.98[EUR][1000 genomes]
rs17670808	0.86[CEU][hapmap];0.83[TSI][hapmap]
rs17738527	0.86[CEU][hapmap];0.83[TSI][hapmap]
rs17738540	0.86[CEU][hapmap];0.83[TSI][hapmap]
rs1807514	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1859479	0.99[EUR][1000 genomes]
rs2412989	0.98[EUR][1000 genomes]
rs2412990	0.99[EUR][1000 genomes]
rs35841307	0.83[EUR][1000 genomes]
rs4820861	0.86[AFR][1000 genomes]
rs5753179	0.88[AFR][1000 genomes]
rs5994313	0.85[AFR][1000 genomes]
rs6518692	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6518693	1.00[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs6518694	0.90[CHB][hapmap];0.82[YRI][hapmap]
rs6518695	0.98[EUR][1000 genomes]
rs7284873	0.84[EUR][1000 genomes]
rs7285878	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7287003	0.81[EUR][1000 genomes]
rs7287135	0.98[EUR][1000 genomes]
rs7287596	0.98[EUR][1000 genomes]
rs7287943	0.94[ASN][1000 genomes]
rs7289820	0.86[CEU][hapmap]
rs7289828	0.84[EUR][1000 genomes]
rs7291870	0.97[EUR][1000 genomes]
rs7292573	0.81[EUR][1000 genomes]
rs737940	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8136225	0.96[EUR][1000 genomes]
rs8136992	0.90[CEU][hapmap];0.97[EUR][1000 genomes]
rs8138569	0.83[AFR][1000 genomes]
rs8138759	0.86[CEU][hapmap];0.83[TSI][hapmap]
rs8141108	0.98[EUR][1000 genomes]
rs8141286	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs8141428	0.97[EUR][1000 genomes]
rs878306	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs886615	0.99[EUR][1000 genomes]
rs886616	0.99[EUR][1000 genomes]
rs886617	0.99[EUR][1000 genomes]
rs9306262	0.97[EUR][1000 genomes]
rs9606735	0.86[CEU][hapmap]
rs9606736	0.85[CEU][hapmap]
rs9606738	0.90[CEU][hapmap];0.83[TSI][hapmap]
rs9606739	0.80[CEU][hapmap]
rs9606744	0.98[EUR][1000 genomes]
rs9606745	0.98[EUR][1000 genomes]
rs9606746	0.82[EUR][1000 genomes]
rs9606747	0.98[EUR][1000 genomes]
rs9606749	0.99[EUR][1000 genomes]
rs9608941	0.86[CEU][hapmap];0.83[TSI][hapmap]
rs9608942	0.86[CEU][hapmap]
rs9608944	0.86[CEU][hapmap]
rs9608946	0.94[ASN][1000 genomes]
rs9608955	0.81[EUR][1000 genomes]
rs9608956	0.95[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs9608960	0.98[EUR][1000 genomes]
rs9608964	0.97[EUR][1000 genomes]
rs9608966	0.98[EUR][1000 genomes]
rs9608967	0.98[EUR][1000 genomes]
rs9608968	0.83[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	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	esv3413089	chr22:30888110-30921604	ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6518698	SEC14L4	cis	cerebellum	SCAN
rs6518698	DUSP18	cis	parietal	SCAN
rs6518698	SEC14L4	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30910200-30922000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr22:30914400-30933400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr22:30918400-30926600	Weak transcription	Gastric	stomach
4	chr22:30921200-30922400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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