Variant report

Variant	rs10983739
Chromosome Location	chr9:98559246-98559247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98555048..98557462-chr9:98559025..98561990,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10121403	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10481647	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10739632	0.96[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10760675	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10760692	0.88[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs10818017	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10983622	0.86[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10983692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10983773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10983818	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12004422	0.85[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12375861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12553442	0.82[ASN][1000 genomes]
rs1410783	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1928253	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2117432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2164156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2164157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2770837	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3930253	0.83[AMR][1000 genomes]
rs583716	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs585223	0.84[AMR][1000 genomes]
rs591579	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs601916	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs615866	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs631273	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs643815	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6478984	0.90[EUR][1000 genomes]
rs6479036	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs676453	0.83[AMR][1000 genomes]
rs680468	0.87[GIH][hapmap];0.83[AMR][1000 genomes]
rs680754	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes]
rs683829	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs689627	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs689749	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs689871	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs689979	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs690222	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs690304	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs690335	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs690455	0.88[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes]
rs690484	0.88[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs700963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7024710	0.88[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes]
rs7868559	0.84[AMR][1000 genomes]
rs7874897	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs816671	0.92[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs816676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs816681	0.96[ASN][1000 genomes]
rs913408	0.83[AMR][1000 genomes]
rs9409321	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9409322	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10983739	LINC00476	cis	Artery Aorta	GTEx
rs10983739	LINC00476	cis	Nerve Tibial	GTEx
rs10983739	LINC00476	cis	lung	GTEx
rs10983739	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs10983739	LINC00476	cis	Adipose Subcutaneous	GTEx
rs10983739	HSD17B3	cis	parietal	SCAN
rs10983739	C9orf130	cis	cerebellum	SCAN
rs10983739	C9orf130	cis	parietal	SCAN
rs10983739	FGD3	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98548400-98578400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:98557400-98563600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr9:98557400-98577200	Weak transcription	Pancreas	Pancrea
4	chr9:98557600-98562600	Weak transcription	HUVEC	blood vessel

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