Variant report

Variant	rs13288354
Chromosome Location	chr9:72164201-72164202
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:72027335..72027966-chr9:72164135..72164934,2	MCF-7	breast:
2	chr9:72036664..72037777-chr9:72163377..72165001,9	K562	blood:
3	chr9:72036895..72038079-chr9:72163773..72164881,7	MCF-7	breast:
4	chr9:72038579..72040872-chr9:72161729..72164338,3	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10511966	1.00[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs10867682	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs10867766	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10867768	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11138902	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs11139065	1.00[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11139155	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11139224	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11139228	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11139236	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11139245	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11139246	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11139274	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11139279	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11139289	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11139293	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11139294	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11139299	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11139300	0.80[AMR][1000 genomes]
rs12378157	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs12378318	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12553491	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13283450	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13286303	0.91[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs13286400	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13287758	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13289730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13290847	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs13291843	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13302431	0.85[EUR][1000 genomes]
rs1330326	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1330331	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1475641	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs1854701	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2297420	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs2777864	0.83[EUR][1000 genomes]
rs35631039	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7025896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7871891	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][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	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	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:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72158800-72166000	Weak transcription	Fetal Heart	heart
2	chr9:72163000-72164400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:72163200-72164400	Enhancers	Brain Cingulate Gyrus	brain
4	chr9:72163200-72164400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:72163200-72164800	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr9:72163200-72185600	Weak transcription	Aorta	Aorta
7	chr9:72163400-72164400	Enhancers	Brain Substantia Nigra	brain
8	chr9:72163400-72164600	Enhancers	Brain Hippocampus Middle	brain
9	chr9:72163600-72164400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:72163600-72164400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr9:72163600-72164400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:72163600-72164600	Enhancers	Brain Angular Gyrus	brain
13	chr9:72163800-72164400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:72163800-72164400	Enhancers	Fetal Muscle Trunk	muscle
15	chr9:72163800-72164600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr9:72164000-72164400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:72164000-72164400	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr9:72164000-72164400	Enhancers	HSMMtube	muscle
19	chr9:72164000-72164600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr9:72164200-72164400	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr9:72164200-72164400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:72164200-72164400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:72164200-72164400	Enhancers	Left Ventricle	heart
24	chr9:72164200-72164400	Bivalent Enhancer	HepG2	liver
25	chr9:72164200-72164400	Flanking Active TSS	Osteobl	bone
26	chr9:72164200-72164600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr9:72164200-72164600	Enhancers	Stomach Mucosa	stomach
28	chr9:72164200-72164800	Enhancers	Liver	Liver

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