Variant report

Variant	rs4523385
Chromosome Location	chr9:100158460-100158461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10122063	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10125198	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1020884	0.97[EUR][1000 genomes]
rs1020885	0.97[EUR][1000 genomes]
rs1037948	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1037950	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1037951	0.96[EUR][1000 genomes]
rs10435867	0.87[ASN][1000 genomes]
rs10435868	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10448274	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10759527	0.84[CEU][hapmap]
rs10759624	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10759657	0.97[EUR][1000 genomes]
rs10817273	0.85[CEU][hapmap]
rs10817286	0.85[CEU][hapmap]
rs10817487	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10981280	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs10981288	0.81[ASW][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10981329	0.81[ASW][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10981890	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10981919	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10981931	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11791310	0.81[ASW][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs13298346	0.81[ASW][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs13299627	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs1542506	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1544203	0.81[ASW][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap]
rs1947717	0.89[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2169456	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap]
rs2219664	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs2242187	0.87[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2279114	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2306097	0.81[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2615143	0.81[ASW][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs2615145	0.81[ASW][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs2795367	0.85[CHB][hapmap]
rs2818238	0.81[ASW][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2818243	0.91[JPT][hapmap]
rs3214072	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs3747489	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3747493	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3747496	0.81[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3802471	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4237189	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4313271	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4366181	0.87[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4554595	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4742685	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4742689	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4742690	0.97[EUR][1000 genomes]
rs4743072	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs4743076	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4743077	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4743084	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4743087	1.00[CEU][hapmap]
rs4743088	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs6478095	0.81[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6478131	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7020393	0.81[JPT][hapmap]
rs7042707	0.81[JPT][hapmap]
rs713066	0.81[ASW][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap]
rs750674	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs7869536	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9696167	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][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	nsv1036105	chr9:100131266-100171816	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4523385	XPA	cis	parietal	SCAN
rs4523385	RP11-498P14.5	cis	lung	GTEx
rs4523385	RP11-498P14.5	cis	Thyroid	GTEx
rs4523385	ECM2	cis	parietal	SCAN
rs4523385	VN1R51P	cis	Thyroid	GTEx
rs4523385	TMOD1	cis	cerebellum	SCAN
rs4523385	RP11-520B13.4	cis	Thyroid	GTEx
rs4523385	RP11-520B13.4	cis	Esophagus Muscularis	GTEx
rs4523385	ANKRD18CP	cis	Thyroid	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100149600-100161400	Weak transcription	Right Atrium	heart
2	chr9:100153000-100159200	Weak transcription	GM12878-XiMat	blood
3	chr9:100154000-100159000	Enhancers	HepG2	liver
4	chr9:100157400-100161800	Weak transcription	Thymus	Thymus
5	chr9:100157800-100162000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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