Variant report

Variant	rs13097548
Chromosome Location	chr3:89230713-89230714
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1040015	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11914680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11914760	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11916891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11919574	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs11921042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11928901	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12486049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs12487141	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12490373	0.82[EUR][1000 genomes]
rs12490659	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12491480	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12493524	0.83[EUR][1000 genomes]
rs12493527	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12494615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12496609	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12496791	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13058761	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13060198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13071923	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074291	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs13075931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs13084503	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13089469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13093815	0.91[YRI][hapmap]
rs13095092	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098003	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13101118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs1512909	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34493897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];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	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34992749	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35053334	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35156943	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35445148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35971332	0.89[ASN][1000 genomes]
rs4132274	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs56408441	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56938121	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59668913	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551395	0.92[YRI][hapmap]
rs6778523	0.82[EUR][1000 genomes]
rs71322851	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322854	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322855	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322856	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322857	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71322858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7430987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7432443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7617920	0.81[AFR][1000 genomes]
rs7631932	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs7635321	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs7637578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap]
rs7638207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7642606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[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	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	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
3	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	chr3:89221600-89233400	Weak transcription	Gastric	stomach
2	chr3:89222600-89233600	Weak transcription	Brain Germinal Matrix	brain
3	chr3:89227200-89235800	Weak transcription	Fetal Brain Female	brain
4	chr3:89228200-89231600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:89228400-89231200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:89228400-89231200	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr3:89228400-89231600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:89228600-89230800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr3:89228600-89231200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:89229000-89230800	Enhancers	Fetal Heart	heart
11	chr3:89229400-89233800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:89229400-89234800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:89229800-89230800	Weak transcription	Fetal Brain Male	brain
14	chr3:89229800-89232400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:89229800-89233400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:89229800-89233800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:89229800-89233800	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:89230000-89233200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:89230000-89233400	Weak transcription	Fetal Lung	lung
20	chr3:89230000-89234000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:89230200-89233400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:89230200-89233600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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