Variant report

Variant	rs16901958
Chromosome Location	chr5:44776556-44776557
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10512866	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951477	0.91[EUR][1000 genomes]
rs11957933	0.91[EUR][1000 genomes]
rs13153376	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13153426	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13162944	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13163070	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13165641	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13165992	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13166622	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13167135	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13167593	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13167624	0.88[AFR][1000 genomes]
rs13172191	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13173899	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13180428	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13183825	0.91[EUR][1000 genomes]
rs13184849	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13185697	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13187122	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13187187	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13188873	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13188895	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16901939	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16901954	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16901986	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16901987	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17343002	1.00[YRI][hapmap]
rs2330571	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34094652	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34098474	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34133773	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34172556	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34216230	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34282174	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34544432	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34918593	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34942360	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35241613	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35278372	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35472604	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35534193	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35564441	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35842403	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35850760	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35868527	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36163058	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4398644	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57288883	0.91[EUR][1000 genomes]
rs58871041	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59337658	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60303396	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60772043	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61695869	1.00[ASN][1000 genomes]
rs6451785	0.91[EUR][1000 genomes]
rs6860030	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6869608	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6870104	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6870510	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6876888	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6877331	0.91[EUR][1000 genomes]
rs6877454	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6881573	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6882983	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891637	0.91[EUR][1000 genomes]
rs6893211	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71590654	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73752417	1.00[ASN][1000 genomes]
rs73752418	1.00[ASN][1000 genomes]
rs7704815	0.91[EUR][1000 genomes]
rs7710153	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7726555	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7735466	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7736197	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880457	chr5:44632008-44800665	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830279	chr5:44688175-44860815	Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv1027897	chr5:44695278-45061623	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
4	nsv597933	chr5:44740989-44810740	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs16901958	SRGAP1	trans	brain	seeQTL
rs16901958	NUFIP2	trans	brain	seeQTL
rs16901958	PHACTR1	trans	brain	seeQTL
rs16901958	ADRBK2	trans	brain	seeQTL
rs16901958	SLC5A3	trans	brain	seeQTL
rs16901958	DDX6	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:44776000-44777400	Genic enhancers	Hela-S3	cervix

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