Variant report

Variant	rs590099
Chromosome Location	chr7:18336338-18336339
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs17138718	0.86[CHB][hapmap]
rs2791299	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2791300	0.81[MKK][hapmap]
rs2960781	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2960783	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581438	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs581820	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs582937	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs587325	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs600846	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs602349	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs604804	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs605866	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs606064	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs610447	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs612977	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs613852	0.95[ASN][1000 genomes]
rs614304	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs621939	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs628095	0.93[ASN][1000 genomes]
rs636246	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs638521	0.93[ASN][1000 genomes]
rs638620	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs639387	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs639424	0.93[ASN][1000 genomes]
rs661144	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs667764	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs680437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs687748	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6950126	0.88[ASN][1000 genomes]
rs6956566	0.88[ASN][1000 genomes]
rs708127	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs880519	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024398	chr7:17630148-18545073	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv538764	chr7:17630148-18545073	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1026629	chr7:17862477-18362404	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1025023	chr7:17865796-18357630	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1030201	chr7:17898410-18491985	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
6	nsv606357	chr7:17938491-18375245	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv606358	chr7:18084843-18416097	Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
8	nsv887810	chr7:18193589-18391557	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv830914	chr7:18196730-18376047	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1029901	chr7:18205779-18387956	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv830916	chr7:18254299-18433349	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv887811	chr7:18295790-18346230	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv32771	chr7:18333448-18337676	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs590099	SP4	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:18331600-18336600	Weak transcription	Aorta	Aorta
2	chr7:18332600-18336600	Enhancers	Primary hematopoietic stem cells	blood
3	chr7:18333000-18337600	Enhancers	Primary B cells from peripheral blood	blood
4	chr7:18333000-18337800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr7:18334600-18345600	Weak transcription	Right Ventricle	heart
6	chr7:18335200-18336600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr7:18335600-18336600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr7:18336000-18336400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr7:18336000-18337000	Enhancers	Primary B cells from cord blood	blood
10	chr7:18336000-18337200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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