Variant report

Variant	rs2006685
Chromosome Location	chr9:97227545-97227546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12342163	0.88[AFR][1000 genomes]
rs2049008	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2277182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2986859	0.84[ASN][1000 genomes]
rs2987115	0.83[ASN][1000 genomes]
rs4434674	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4477096	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4497033	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4509403	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4743953	0.82[ASN][1000 genomes]
rs4743954	0.86[ASN][1000 genomes]
rs4743955	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4744346	0.86[ASN][1000 genomes]
rs600442	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6479544	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs684892	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7020879	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7023744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7023915	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7024159	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7025755	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7027465	0.84[ASN][1000 genomes]
rs7027489	0.80[ASN][1000 genomes]
rs7031088	0.84[ASN][1000 genomes]
rs7031496	0.86[ASN][1000 genomes]
rs7031949	0.84[ASN][1000 genomes]
rs7037190	0.84[ASN][1000 genomes]
rs7037198	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7040577	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7040710	0.84[ASN][1000 genomes]
rs7047279	0.89[ASN][1000 genomes]
rs7047295	0.87[ASN][1000 genomes]
rs7047930	0.86[ASN][1000 genomes]
rs7048688	0.84[ASN][1000 genomes]
rs7848221	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7848227	0.86[ASN][1000 genomes]
rs7853182	0.81[ASN][1000 genomes]
rs7860616	0.86[ASN][1000 genomes]
rs7863310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868562	0.85[ASN][1000 genomes]
rs9299421	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9299422	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9409552	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9409759	0.86[ASN][1000 genomes]
rs9409763	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9409765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9409777	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9409779	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9777207	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers 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	18 gene(s)	inside rSNPs	diseases
2	nsv1046906	chr9:96999227-97239809	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv893593	chr9:97196979-97228918	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	esv1840205	chr9:97202200-97366400	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv893594	chr9:97221463-97283226	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2006685	RP11-307E17.8	cis	Esophagus Muscularis	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97222600-97237800	Weak transcription	Stomach Mucosa	stomach
2	chr9:97224400-97227800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr9:97225200-97228000	Weak transcription	HMEC	breast
4	chr9:97225400-97228000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr9:97225400-97228200	Weak transcription	NHEK	skin
6	chr9:97225800-97227600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr9:97225800-97227800	Weak transcription	HSMM	muscle

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