Variant report

Variant	rs72877406
Chromosome Location	chr3:59501516-59501517
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs17060878	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17060879	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17060883	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35500604	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58468498	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61553534	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72875698	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72877405	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72877416	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72877418	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72877424	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72877430	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72877432	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72877434	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72877442	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72877443	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72877447	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72877448	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72877450	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72877453	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72877456	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72877460	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7638203	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7646357	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9832635	0.82[ASN][1000 genomes]
rs9865729	0.82[ASN][1000 genomes]
rs9869699	0.82[ASN][1000 genomes]
rs9870039	0.82[ASN][1000 genomes]
rs9871940	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011181	chr3:58665373-59542339	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv536574	chr3:58665373-59542339	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv534257	chr3:58855959-59606464	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv998676	chr3:59485915-59519363	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv876836	chr3:59500394-59664687	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59499600-59503200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:59500200-59503800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr3:59500400-59501600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:59500600-59501600	Flanking Active TSS	Dnd41	blood
5	chr3:59500600-59501800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:59500600-59501800	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr3:59500600-59502200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr3:59500800-59502000	Enhancers	Brain Hippocampus Middle	brain
9	chr3:59501000-59502000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:59501000-59502000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:59501000-59502000	Enhancers	Brain Substantia Nigra	brain
12	chr3:59501000-59502000	Enhancers	Fetal Brain Female	brain
13	chr3:59501000-59502200	Enhancers	Brain Cingulate Gyrus	brain
14	chr3:59501200-59501600	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr3:59501200-59501800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:59501200-59502000	Enhancers	Brain Germinal Matrix	brain
17	chr3:59501200-59502000	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr3:59501200-59502200	Enhancers	H1 Cell Line	embryonic stem cell
19	chr3:59501200-59502800	Weak transcription	Primary T cells from cord blood	blood
20	chr3:59501200-59503600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:59501400-59501800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:59501400-59502200	Enhancers	Brain Anterior Caudate	brain
23	chr3:59501400-59502800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:59501400-59503800	Enhancers	Fetal Lung	lung

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