Variant report

Variant	rs9880889
Chromosome Location	chr3:23489512-23489513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs17013266	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2017065	0.88[CEU][hapmap]
rs2173058	0.88[CEU][hapmap]
rs2359765	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2359766	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2359768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4340647	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57192920	0.93[EUR][1000 genomes]
rs59687869	0.94[EUR][1000 genomes]
rs6764347	0.85[ASN][1000 genomes]
rs73821808	0.95[EUR][1000 genomes]
rs73821809	0.95[EUR][1000 genomes]
rs73821812	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7613185	0.89[CEU][hapmap]
rs7627380	0.88[CEU][hapmap]
rs7627525	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs7628372	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs7639266	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9873929	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9883870	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv876625	chr3:23390301-23509597	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 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	chr3:23473800-23494000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr3:23479800-23490200	Weak transcription	Brain Substantia Nigra	brain
3	chr3:23483200-23491200	Weak transcription	Psoas Muscle	Psoas
4	chr3:23484800-23496000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:23484800-23496000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:23485200-23490200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:23485200-23490600	Weak transcription	Primary B cells from cord blood	blood
8	chr3:23485200-23496400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:23485200-23498600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr3:23486200-23494000	Weak transcription	HSMMtube	muscle
11	chr3:23487200-23491000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:23488000-23490000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:23488400-23489800	Enhancers	GM12878-XiMat	blood
14	chr3:23488600-23490400	Weak transcription	Brain Angular Gyrus	brain
15	chr3:23488600-23491400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:23488600-23496000	Weak transcription	Fetal Heart	heart
17	chr3:23488600-23496200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:23488600-23496400	Weak transcription	Ovary	ovary
19	chr3:23488800-23489600	Enhancers	Brain Hippocampus Middle	brain
20	chr3:23489000-23490000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:23489000-23490000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:23489200-23490600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:23489200-23491400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:23489400-23489800	Enhancers	Right Ventricle	heart

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