Variant report

Variant	rs56408441
Chromosome Location	chr3:89219532-89219533
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1040015	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11914760	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11916891	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928901	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12487141	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12490373	0.82[EUR][1000 genomes]
rs12490659	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12491480	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12493524	0.83[EUR][1000 genomes]
rs12493527	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12494615	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495783	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12496609	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12496791	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13058761	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058886	1.00[EUR][1000 genomes]
rs13060198	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13071923	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074291	0.83[EUR][1000 genomes]
rs13084503	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13089469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095092	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097212	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097548	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098003	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34493897	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34638812	0.82[EUR][1000 genomes]
rs34855223	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34893903	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34992749	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35053334	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35156943	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35445148	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35971332	0.89[ASN][1000 genomes]
rs56938121	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59668913	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778523	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71322851	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322854	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322855	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322856	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322857	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71322858	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7430987	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638207	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7642606	0.91[EUR][1000 genomes];0.92[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	nsv834760	chr3:89085529-89299398	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1005603	chr3:89174152-89223459	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv997874	chr3:89188275-89279573	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1008916	chr3:89206065-89241915	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89215200-89221000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr3:89215200-89221000	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:89215200-89221400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:89215600-89221200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:89216200-89220400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:89216200-89220800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:89216200-89221000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:89216200-89221000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:89216800-89220800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:89217000-89223400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:89217400-89220400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:89217400-89220400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:89217400-89220800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:89217400-89221400	Weak transcription	Brain Angular Gyrus	brain
15	chr3:89217400-89222400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:89217600-89220800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:89217600-89220800	Weak transcription	Brain Germinal Matrix	brain
18	chr3:89218200-89220800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:89218200-89220800	Weak transcription	Brain Anterior Caudate	brain
20	chr3:89218400-89219600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:89218400-89220400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:89219000-89219800	Enhancers	Fetal Brain Male	brain

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