Variant report

Variant	rs12540049
Chromosome Location	chr7:147728115-147728116
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10227736	1.00[CEU][hapmap]
rs10229688	1.00[CEU][hapmap]
rs10253762	1.00[CEU][hapmap]
rs10261595	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs10261693	0.89[JPT][hapmap]
rs10269138	1.00[CEU][hapmap]
rs10269257	1.00[CEU][hapmap]
rs10276996	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs10281326	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs10452891	1.00[CEU][hapmap]
rs10485853	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs10500194	1.00[CEU][hapmap]
rs12530525	1.00[CEU][hapmap]
rs12532080	1.00[CEU][hapmap]
rs12532103	1.00[CEU][hapmap]
rs12532213	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs12533565	0.95[ASN][1000 genomes]
rs12536135	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs12536614	1.00[CEU][hapmap]
rs12539425	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs12539685	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12540014	1.00[CEU][hapmap]
rs12540218	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12667420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13225246	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13225250	1.00[CEU][hapmap]
rs13225815	1.00[CEU][hapmap]
rs13228312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13228553	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13228704	1.00[CEU][hapmap]
rs13233277	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap]
rs13236734	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13236937	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs13238527	1.00[CEU][hapmap]
rs17170767	1.00[CEU][hapmap]
rs17170789	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17170792	0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17170793	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17170794	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2373278	1.00[CEU][hapmap]
rs2373280	1.00[CEU][hapmap]
rs2373286	1.00[CEU][hapmap]
rs34378091	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34842703	0.92[ASN][1000 genomes]
rs34910390	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34987081	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35100395	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35275476	0.84[ASN][1000 genomes]
rs35294118	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35442317	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35631331	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57783871	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62473287	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62473288	0.81[EUR][1000 genomes]
rs62473289	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62473290	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6947287	1.00[CEU][hapmap]
rs6947595	1.00[CEU][hapmap]
rs6955458	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6957073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6962266	1.00[CEU][hapmap]
rs719310	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs719311	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs719312	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7779961	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs7781064	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7781680	0.95[CHB][hapmap];0.80[JPT][hapmap];0.92[ASN][1000 genomes]
rs7785350	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs7789579	1.00[CEU][hapmap]
rs7797584	1.00[CEU][hapmap]
rs7800075	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs7805706	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023913	chr7:147521075-147806318	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1026058	chr7:147521109-147783042	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv539179	chr7:147521109-147783042	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv934002	chr7:147521110-147807705	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1017610	chr7:147523752-147806427	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2558199	chr7:147726823-147728311	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	n/a

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:147727800-147728200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:147728000-147728200	Enhancers	H9 Cell Line	embryonic stem cell
3	chr7:147728000-147728200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
4	chr7:147728000-147728200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
5	chr7:147728000-147728600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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