Variant report

Variant	rs11589719
Chromosome Location	chr1:86352629-86352630
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11161674	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs11578980	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11588668	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11589722	1.00[CHB][hapmap]
rs11799965	0.92[CHB][hapmap]
rs11801550	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs11803202	0.93[CHB][hapmap]
rs11811165	0.92[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes]
rs12562000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12564528	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12567327	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12569293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12755267	1.00[CHB][hapmap]
rs17128505	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17128521	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2062760	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753785	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs7551256	1.00[CEU][hapmap]
rs7556366	1.00[CHB][hapmap]

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	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546721	chr1:86226352-86392577	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv999743	chr1:86241246-86364846	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1011293	chr1:86270649-86416972	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv871189	chr1:86315724-86402244	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv1810714	chr1:86339811-86392577	Weak transcription Enhancers ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11589719	SAA3P	trans	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86342400-86370600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:86345600-86370600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:86347000-86366000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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