Variant report

Variant	rs9888507
Chromosome Location	chr13:40037288-40037289
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10492734	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10492735	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10492736	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10492737	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12583299	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12583316	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12583320	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12583364	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12583486	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12583593	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12584059	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12584451	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12584721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12586018	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12873765	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17059971	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17059988	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17060000	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17060022	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17068651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35613729	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57594426	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59403463	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59798386	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60199520	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73175139	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73175140	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73175141	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73175149	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7325544	0.85[EUR][1000 genomes]
rs7990728	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7990910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7995349	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7996490	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7999971	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8000564	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv561536	chr13:40015948-40043224	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40032600-40038000	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr13:40034000-40041200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr13:40034800-40037400	Enhancers	Placenta Amnion	Placenta Amnion
4	chr13:40035600-40038000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr13:40035600-40038200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr13:40036400-40039800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:40036800-40037400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr13:40036800-40037400	Enhancers	Aorta	Aorta
9	chr13:40036800-40038000	Enhancers	Right Ventricle	heart
10	chr13:40036800-40038400	Enhancers	Fetal Heart	heart
11	chr13:40037000-40038000	Enhancers	Right Atrium	heart
12	chr13:40037000-40051200	Weak transcription	Ovary	ovary
13	chr13:40037000-40053800	Weak transcription	Fetal Lung	lung
14	chr13:40037200-40039800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr13:40037200-40039800	Weak transcription	Left Ventricle	heart
16	chr13:40037200-40043400	Weak transcription	Psoas Muscle	Psoas
17	chr13:40037200-40045000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr13:40037200-40045000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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