Variant report

Variant	rs17005056
Chromosome Location	chr4:82029505-82029506
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17005057	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17005061	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2028644	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55864419	0.96[EUR][1000 genomes]
rs56193456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56292411	1.00[EUR][1000 genomes]
rs59402330	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6817213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847955	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6850736	0.95[EUR][1000 genomes]
rs72663821	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72663823	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72663824	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72663826	1.00[EUR][1000 genomes]
rs72663827	0.96[EUR][1000 genomes]
rs72663829	0.95[EUR][1000 genomes]
rs894746	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs980720	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[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	nsv999729	chr4:81802554-82627820	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537156	chr4:81802554-82627820	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv829984	chr4:81979988-82113977	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	esv1822437	chr4:82025743-82118996	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17005056	RAGE	trans	lymphoblastoid	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:81998200-82030000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:82013000-82033200	Weak transcription	NHLF	lung
3	chr4:82025400-82051600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:82027800-82032600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr4:82028000-82032800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:82028200-82035000	Weak transcription	NHDF-Ad	bronchial
7	chr4:82028200-82050600	Weak transcription	Fetal Intestine Large	intestine
8	chr4:82028600-82030000	Strong transcription	Fetal Intestine Small	intestine
9	chr4:82028600-82030800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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