Variant report

Variant	rs6801444
Chromosome Location	chr3:160595420-160595421
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10154889	0.95[CEU][hapmap]
rs10433352	0.81[CEU][hapmap]
rs11711152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11713093	0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs11718966	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11916355	0.86[EUR][1000 genomes]
rs13071999	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13073059	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13315565	0.94[CEU][hapmap]
rs1345156	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1447610	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1447622	1.00[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1562464	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs16831563	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16831796	0.81[CEU][hapmap]
rs1839016	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1868105	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1868107	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2044571	1.00[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs2197700	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2889390	0.80[CEU][hapmap]
rs35257491	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4679920	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441337	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6441338	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66872845	0.83[EUR][1000 genomes]
rs6768115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7624185	1.00[CEU][hapmap]
rs7628389	0.81[CEU][hapmap]
rs7641892	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs898677	0.81[CEU][hapmap]
rs935497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs964533	1.00[CEU][hapmap]
rs9812507	1.00[CEU][hapmap]
rs9822435	1.00[CEU][hapmap]
rs9832109	1.00[CEU][hapmap]
rs9844267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9845943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9857482	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9857855	0.85[CEU][hapmap]
rs9860537	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9871801	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9876142	0.90[CEU][hapmap]
rs9883566	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv32963	chr3:160555238-160603116	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6801444	SPTSSB	cis	Thyroid	GTEx
rs6801444	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160589000-160596000	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:160591800-160595600	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr3:160592200-160595600	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr3:160594600-160596200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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