Variant report

Variant	rs9311469
Chromosome Location	chr3:51540035-51540036
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1031925	1.00[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1055429	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10865970	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11130292	0.80[AMR][1000 genomes]
rs11130293	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721253	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917683	1.00[CEU][hapmap]
rs11919197	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap]
rs13090011	0.85[CEU][hapmap]
rs1383251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1480353	1.00[CEU][hapmap]
rs1480354	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1542574	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1552074	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17051734	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs17051762	0.91[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2127655	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2164599	0.82[EUR][1000 genomes]
rs2219890	1.00[CEU][hapmap]
rs3821829	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4067	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap]
rs4234644	1.00[CEU][hapmap]
rs4317086	0.82[AMR][1000 genomes]
rs4355273	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4611808	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687568	0.86[AMR][1000 genomes]
rs4687569	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4687721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687734	0.86[AMR][1000 genomes]
rs4974104	1.00[CEU][hapmap]
rs4974105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4974106	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6445620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs6445622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap]
rs6445628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6445791	0.82[AMR][1000 genomes]
rs6771491	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6775666	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap]
rs6787312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes]
rs6793900	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6809155	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7372658	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs751075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7625006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7625821	0.81[EUR][1000 genomes]
rs7633708	0.84[CEU][hapmap]
rs7648012	0.92[CEU][hapmap]

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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9311469	TEX264	cis	Esophagus Muscularis	GTEx
rs9311469	IQCF2	cis	parietal	SCAN
rs9311469	TEX264	cis	Nerve Tibial	GTEx
rs9311469	HYAL2	cis	parietal	SCAN
rs9311469	TEX264	cis	Artery Tibial	GTEx
rs9311469	TEX264	cis	Esophagus Mucosa	GTEx
rs9311469	HEMK1	cis	cerebellum	SCAN
rs9311469	MST1	cis	cerebellum	SCAN
rs9311469	NCKIPSD	cis	cerebellum	SCAN
rs9311469	PARP3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51535000-51541400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:51536200-51540200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:51536400-51543200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr3:51537000-51543800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:51538000-51543400	Weak transcription	Placenta	Placenta

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