Variant report

Variant	rs4743088
Chromosome Location	chr9:100158815-100158816
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TSTD2-4	chr9:100158779-100158973	NONHSAT133504
2	lnc-TSTD2-4	chr9:100158779-100158947	NONHSAT133503
3	lnc-TSTD2-4	chr9:100158779-100158973	XLOC_007795

Extended variants
information (count: 64 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10122063	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs10125198	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs1020884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1020885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1037948	0.91[EUR][1000 genomes]
rs1037950	0.97[EUR][1000 genomes]
rs1037951	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10435868	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs10448274	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs10759527	0.84[CEU][hapmap];0.95[CHB][hapmap]
rs10759624	0.90[EUR][1000 genomes]
rs10759657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817273	0.85[CEU][hapmap];0.95[CHB][hapmap]
rs10817286	0.85[CEU][hapmap];0.95[CHB][hapmap]
rs10817487	0.91[EUR][1000 genomes]
rs10981367	0.85[JPT][hapmap]
rs10981460	0.85[JPT][hapmap]
rs10981890	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs10981919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10981931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12377538	0.85[JPT][hapmap]
rs12550923	0.85[JPT][hapmap]
rs12551740	0.85[JPT][hapmap]
rs13287082	0.85[JPT][hapmap]
rs13289134	0.85[JPT][hapmap]
rs1531440	0.85[JPT][hapmap]
rs1542506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1947717	0.89[CEU][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs2045729	0.85[JPT][hapmap]
rs2169456	0.96[CEU][hapmap]
rs2242187	0.96[CEU][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs2279114	0.95[EUR][1000 genomes]
rs2290933	0.85[JPT][hapmap]
rs2306094	0.85[JPT][hapmap]
rs2306097	0.96[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs3747489	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs3747493	0.96[CEU][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs3747495	0.85[JPT][hapmap]
rs3747496	0.96[CEU][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs3747498	0.85[JPT][hapmap]
rs3747499	0.85[JPT][hapmap]
rs3747504	0.85[JPT][hapmap]
rs3747506	0.85[JPT][hapmap]
rs3802471	0.92[EUR][1000 genomes]
rs3994560	0.85[JPT][hapmap]
rs4237189	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs4313271	0.96[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs4366181	0.96[CEU][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs4523385	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs4554595	0.91[EUR][1000 genomes]
rs4742685	0.89[EUR][1000 genomes]
rs4742689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742690	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743070	0.85[JPT][hapmap]
rs4743073	0.85[JPT][hapmap]
rs4743076	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4743077	0.96[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs4743084	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs4743087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6478095	0.96[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs6478131	0.95[EUR][1000 genomes]
rs7869536	0.95[EUR][1000 genomes]
rs9696167	0.91[EUR][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4743088	ECM2	cis	parietal	SCAN
rs4743088	ANKRD18CP	cis	Thyroid	GTEx
rs4743088	RP11-498P14.5	cis	lung	GTEx
rs4743088	XPA	cis	parietal	SCAN
rs4743088	TMOD1	cis	cerebellum	SCAN
rs4743088	RP11-520B13.4	cis	Esophagus Muscularis	GTEx
rs4743088	VN1R51P	cis	Thyroid	GTEx
rs4743088	RP11-520B13.4	cis	Thyroid	GTEx

Chromatin state (count:6 , 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
6	chr9:100158800-100159000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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