Variant report

Variant	rs9606747
Chromosome Location	chr22:30912328-30912329
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1001409	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1008801	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11912737	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11914168	1.00[JPT][hapmap]
rs12165604	0.86[EUR][1000 genomes]
rs12484688	1.00[JPT][hapmap]
rs13053262	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13053759	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13054004	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13054381	0.81[AMR][1000 genomes]
rs13750	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16988720	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16988803	1.00[JPT][hapmap]
rs16988810	1.00[JPT][hapmap]
rs16988814	1.00[JPT][hapmap]
rs17670707	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17670808	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17738527	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17738540	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1807514	0.99[EUR][1000 genomes]
rs1859479	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1986969	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2023967	0.91[AMR][1000 genomes]
rs2189835	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2412989	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412990	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35102600	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35530794	1.00[ASN][1000 genomes]
rs35841307	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4602314	1.00[ASN][1000 genomes]
rs4820019	1.00[JPT][hapmap]
rs4820869	1.00[JPT][hapmap]
rs4820874	1.00[JPT][hapmap]
rs60308761	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6518692	0.99[EUR][1000 genomes]
rs6518693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6518695	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6518698	0.98[EUR][1000 genomes]
rs7284873	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7285878	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7286523	1.00[ASN][1000 genomes]
rs7286807	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7287003	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7287135	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7287596	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7289277	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7289820	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7289828	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7291870	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7292573	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737940	0.97[EUR][1000 genomes]
rs737942	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8136225	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8136992	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8137267	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8137718	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8138759	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8141108	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8141286	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8141318	1.00[ASN][1000 genomes]
rs8141428	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8141671	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs878306	0.98[EUR][1000 genomes]
rs886615	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886616	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886617	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306262	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606735	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9606736	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9606738	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9606739	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9606744	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606745	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606746	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606749	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608935	1.00[ASN][1000 genomes]
rs9608936	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9608938	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9608940	1.00[ASN][1000 genomes]
rs9608941	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9608942	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9608944	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9608955	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608956	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9608960	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608964	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608966	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608967	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608968	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608972	0.88[AMR][1000 genomes];0.91[ASN][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
rs9606747	SEC14L4	cis	cerebellum	SCAN
rs9606747	DUSP18	cis	parietal	SCAN
rs9606747	SEC14L4	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30910000-30912400	Enhancers	HepG2	liver
2	chr22:30910200-30922000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr22:30911600-30912800	Enhancers	Lung	lung
4	chr22:30912200-30913200	Enhancers	K562	blood

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