Variant report

Variant	rs623419
Chromosome Location	chr2:31834078-31834079
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12467911	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs2208532	0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2268799	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2300697	0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2300699	0.81[AMR][1000 genomes]
rs2300701	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs2754530	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4952197	0.82[CHB][hapmap]
rs499362	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs502139	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs522638	0.88[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs523349	0.87[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs524345	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs527112	0.91[ASN][1000 genomes]
rs539213	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs553464	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs559555	0.86[ASN][1000 genomes]
rs569320	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs589427	0.88[ASN][1000 genomes]
rs599300	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs607294	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs608574	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs632148	0.86[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs676033	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs681482	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs682895	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs765138	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs806645	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv998853	chr2:31601455-31858961	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1005565	chr2:31603134-31868877	Genic enhancers Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1007179	chr2:31616112-31835410	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1005032	chr2:31616112-31867450	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1013891	chr2:31629179-31854283	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv535612	chr2:31629179-31854283	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1002988	chr2:31767131-31996924	Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv961024	chr2:31814613-31870845	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs623419	SLC30A6	cis	parietal	SCAN
rs623419	SLC30A6	cis	cerebellum	SCAN
rs623419	NLRC4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31833200-31835600	Weak transcription	Liver	Liver

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