Variant report

Variant	rs17729489
Chromosome Location	chr3:70109148-70109149
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1027234	0.81[ASN][1000 genomes]
rs11923982	0.85[AMR][1000 genomes]
rs12495615	0.85[AMR][1000 genomes]
rs1491694	0.82[CHB][hapmap];0.96[JPT][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1491696	0.80[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1491697	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1491700	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17729465	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17785152	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes]
rs17785756	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2101636	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2874269	0.84[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3849467	0.82[AMR][1000 genomes]
rs4855334	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4855335	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55966844	0.85[AMR][1000 genomes]
rs60251138	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs60403843	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61645126	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6549267	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6763730	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6799525	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7431273	0.86[AMR][1000 genomes]
rs7611660	0.80[CHB][hapmap];0.86[YRI][hapmap]
rs7619924	0.92[CEU][hapmap];0.86[CHB][hapmap];0.96[JPT][hapmap];0.81[AMR][1000 genomes]
rs7632596	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7645353	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7649560	0.92[CEU][hapmap];0.97[YRI][hapmap];0.85[AMR][1000 genomes]
rs7651972	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9310181	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9815027	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9818798	0.81[AMR][1000 genomes]
rs9818964	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9826811	0.80[AMR][1000 genomes]
rs9837453	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9840951	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9843867	0.81[AMR][1000 genomes]
rs9856462	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[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	nsv533396	chr3:69964029-70538306	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17729489	RP11-460N16.1	cis	Artery Aorta	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:70107400-70112200	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr3:70107400-70112600	Weak transcription	Fetal Brain Male	brain
3	chr3:70107400-70116800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:70107400-70120400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:70107600-70112600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:70107600-70112600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:70107600-70120200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:70107800-70112400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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