Variant report

Variant	rs6789219
Chromosome Location	chr3:53098938-53098939
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SFMBT1-2	chr3:53098299-53099107	NONHSAT089979

Extended variants
information (count: 57 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11130332	0.86[EUR][1000 genomes]
rs1134546	1.00[CEU][hapmap]
rs11707576	0.87[EUR][1000 genomes]
rs11708223	0.86[EUR][1000 genomes]
rs13082061	0.85[EUR][1000 genomes]
rs17304995	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2246556	0.84[CEU][hapmap]
rs2255107	0.81[CEU][hapmap]
rs2336669	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2336671	0.85[EUR][1000 genomes]
rs2564947	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2581779	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2581780	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2581796	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2581797	0.86[EUR][1000 genomes]
rs2581801	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2581802	0.86[EUR][1000 genomes]
rs2581805	0.86[EUR][1000 genomes]
rs2581810	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2581815	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2581820	0.89[EUR][1000 genomes]
rs2581823	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2710345	0.86[EUR][1000 genomes]
rs34230854	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35380116	0.84[EUR][1000 genomes]
rs4302374	0.94[CEU][hapmap]
rs4519686	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4687692	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4687699	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59989280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445547	0.93[CEU][hapmap]
rs6445550	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6768844	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6770957	0.88[EUR][1000 genomes]
rs6771610	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6792578	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6805298	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71301803	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71301807	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7621939	0.87[EUR][1000 genomes]
rs7637082	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7644973	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7648514	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7652131	0.88[EUR][1000 genomes]
rs9311485	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9812543	0.88[EUR][1000 genomes]
rs9813024	0.84[EUR][1000 genomes]
rs9831409	0.86[EUR][1000 genomes]
rs9842974	0.88[EUR][1000 genomes]
rs9844736	1.00[CEU][hapmap]
rs9846976	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9847024	0.81[EUR][1000 genomes]
rs9865094	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9870240	0.88[ASN][1000 genomes]
rs9870898	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876403	0.93[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	nsv876800	chr3:53038786-53113762	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6789219	ITIH4-AS1	cis	Artery Aorta	GTEx
rs6789219	ITIH4-AS1	cis	Artery Tibial	GTEx
rs6789219	ITIH4	Cis_1M	lymphoblastoid	RTeQTL
rs6789219	ITIH4-AS1	cis	lung	GTEx
rs6789219	SERBP1P3	cis	lung	GTEx
rs6789219	MUSTN1	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53098400-53106000	Weak transcription	Spleen	Spleen

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