Variant report

Variant	rs4433402
Chromosome Location	chr1:221946172-221946173
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10218652	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779456	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10863653	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10863655	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10863656	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11118844	0.82[AMR][1000 genomes]
rs11118847	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11118848	0.92[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs11118854	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118857	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11118859	0.98[EUR][1000 genomes]
rs11118860	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs12070192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136350	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12144586	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12403995	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17010720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4073062	0.83[EUR][1000 genomes]
rs4589119	0.92[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs4601596	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs4623704	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs58850477	0.84[EUR][1000 genomes]
rs66522549	0.82[AMR][1000 genomes]
rs6655994	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6665052	0.93[ASN][1000 genomes]
rs6665466	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7516292	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7518806	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription 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	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking 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	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1007092	chr1:221883491-221958279	Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv535303	chr1:221883491-221958279	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4433402	RAB3GAP2	cis	parietal	SCAN
rs4433402	USH2A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221942800-221947400	Weak transcription	HUVEC	blood vessel
2	chr1:221944600-221947400	Enhancers	Hela-S3	cervix
3	chr1:221945000-221946400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:221945000-221946400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr1:221945200-221946400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:221945200-221946400	Enhancers	GM12878-XiMat	blood
7	chr1:221945400-221949600	Weak transcription	Rectal Mucosa Donor 31	rectum

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