Variant report

Variant	rs6551398
Chromosome Location	chr3:89213269-89213270
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11128070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12494816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13077331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434229	0.88[EUR][1000 genomes]
rs56895676	0.91[EUR][1000 genomes]
rs57618914	0.91[EUR][1000 genomes]
rs58716947	0.88[EUR][1000 genomes]
rs58987133	0.91[EUR][1000 genomes]
rs59083916	0.88[EUR][1000 genomes]
rs59111523	0.91[EUR][1000 genomes]
rs59800917	0.91[EUR][1000 genomes]
rs60573712	0.88[EUR][1000 genomes]
rs61000929	0.88[EUR][1000 genomes]
rs61253060	0.91[EUR][1000 genomes]
rs6551395	0.89[JPT][hapmap]
rs6551399	0.83[AMR][1000 genomes]
rs6551406	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6551408	0.83[AMR][1000 genomes]
rs6767230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6779710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6790662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67935343	0.85[EUR][1000 genomes]
rs6793981	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];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6797343	0.89[JPT][hapmap]
rs6800287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6804377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6807840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7373480	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73845930	0.90[EUR][1000 genomes]
rs73845931	0.90[EUR][1000 genomes]
rs73845942	0.88[EUR][1000 genomes]
rs73845947	0.91[EUR][1000 genomes]
rs73845948	0.91[EUR][1000 genomes]
rs7426466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7426527	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7427745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7427935	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7622368	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7632543	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7633559	0.87[JPT][hapmap]
rs7636079	0.83[AMR][1000 genomes]
rs7651124	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7652840	0.83[AMR][1000 genomes]
rs9310113	0.89[JPT][hapmap]
rs9810701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9811026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9814718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9828822	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]
rs9829805	0.83[AMR][1000 genomes]
rs9834135	0.89[ASN][1000 genomes]
rs9835264	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9859735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860030	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9861649	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];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9868041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9883722	1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][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:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89211600-89217400	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr3:89211800-89213400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:89211800-89213600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:89212000-89213600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:89212200-89213600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:89212200-89213800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:89212200-89214000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:89212200-89215000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:89213200-89215000	Enhancers	HUES64 Cell Line	embryonic stem cell

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