Variant report

Variant	rs3008600
Chromosome Location	chr1:222780592-222780593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1986348	0.83[EUR][1000 genomes]
rs2936019	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2936024	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2936025	0.85[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2936026	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2936055	0.89[ASN][1000 genomes]
rs2936056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2936057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3002137	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3002140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3002150	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3008598	0.84[JPT][hapmap]
rs3008599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3008603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3008605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3008611	0.85[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3008613	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3008624	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3008627	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3008628	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3008632	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3008635	0.85[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3008639	0.85[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs34290674	0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs4379681	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73124815	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73124822	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73124862	0.80[AMR][1000 genomes]
rs73124880	0.83[EUR][1000 genomes]
rs73124889	0.83[EUR][1000 genomes]
rs73126803	0.83[EUR][1000 genomes]
rs73126812	0.83[EUR][1000 genomes]
rs73126814	0.83[EUR][1000 genomes]

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	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3008600	BROX	cis	lymphoblastoid	seeQTL
rs3008600	C1orf58	cis	multi-tissue	Pritchard

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222780000-222780600	Enhancers	Stomach Mucosa	stomach
2	chr1:222780400-222781200	Enhancers	Rectal Mucosa Donor 31	rectum

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