Variant report

Variant	rs6559625
Chromosome Location	chr9:72153844-72153845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10217407	0.81[CHB][hapmap]
rs10283713	0.81[CHB][hapmap]
rs10283788	0.80[CHB][hapmap]
rs1029065	0.81[CHB][hapmap]
rs10481750	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10780507	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10867647	0.81[CHB][hapmap]
rs10867671	0.81[CHB][hapmap]
rs10867672	0.81[CHB][hapmap]
rs10867730	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10867757	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1113067	0.81[CHB][hapmap]
rs11138927	0.81[CHB][hapmap]
rs11138980	0.81[CHB][hapmap]
rs11138986	0.81[CHB][hapmap]
rs11139043	0.81[CHB][hapmap]
rs11139050	0.81[CHB][hapmap]
rs11139063	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap]
rs11139084	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11139269	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11788742	0.81[CHB][hapmap]
rs12235168	0.81[CHB][hapmap]
rs12344522	0.81[CHB][hapmap]
rs12348063	0.81[CHB][hapmap]
rs1330327	0.95[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1330328	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1330330	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1331979	0.81[CHB][hapmap]
rs2285080	0.96[ASN][1000 genomes]
rs2297421	0.81[CHB][hapmap]
rs3897966	0.81[CHB][hapmap]
rs4744570	0.81[CHB][hapmap]
rs4744908	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6559626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7019109	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7025471	0.95[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7033083	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7044071	0.81[CHB][hapmap]
rs7044971	0.95[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7046404	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7357615	0.81[CHB][hapmap]
rs7851858	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7858003	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865302	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1035633	chr9:71995963-72176984	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1048650	chr9:72028458-72179847	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1039966	chr9:72057304-72181564	Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv466413	chr9:72100051-72160174	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv614575	chr9:72100051-72160174	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv893437	chr9:72118962-72223176	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72132200-72163000	Weak transcription	Aorta	Aorta
2	chr9:72141800-72158200	Weak transcription	Ovary	ovary
3	chr9:72143600-72158400	Weak transcription	Liver	Liver
4	chr9:72146600-72157000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:72147600-72158200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:72148600-72157000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr9:72151200-72157400	Weak transcription	Brain Germinal Matrix	brain
8	chr9:72153200-72156400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr9:72153400-72157000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr9:72153800-72154000	Active TSS	Spleen	Spleen

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