Variant report

Variant	rs1925827
Chromosome Location	chr1:62759076-62759077
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10157938	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs10465842	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493318	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs10889318	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11207955	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs11207956	0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs12031176	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs12038843	0.86[JPT][hapmap]
rs12123763	0.80[EUR][1000 genomes]
rs12138544	0.86[JPT][hapmap]
rs12749514	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1325738	0.85[CEU][hapmap]
rs1325740	0.89[ASN][1000 genomes]
rs1886830	0.85[CEU][hapmap]
rs1886833	0.91[ASN][1000 genomes]
rs1886834	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1925825	0.86[CEU][hapmap]
rs2366207	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2477874	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666467	0.86[CEU][hapmap]
rs2666509	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2765260	0.86[CEU][hapmap]
rs2765262	0.85[CEU][hapmap]
rs2765266	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765268	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765269	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35126231	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3850632	0.85[CEU][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3861936	0.85[JPT][hapmap]
rs4915606	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4915607	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587966	0.87[ASN][1000 genomes]
rs6658312	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675508	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6675627	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7514266	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881548	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs9803815	0.81[CEU][hapmap];0.86[JPT][hapmap]

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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62753200-62760000	Weak transcription	Fetal Stomach	stomach
2	chr1:62753200-62761600	Weak transcription	Pancreas	Pancrea
3	chr1:62753200-62761600	Weak transcription	Right Atrium	heart
4	chr1:62754200-62760200	Weak transcription	Placenta	Placenta
5	chr1:62754400-62773400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:62754800-62765200	Weak transcription	Fetal Heart	heart
7	chr1:62755000-62759800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:62755200-62759800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:62755600-62761000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:62756200-62765000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:62756400-62764800	Weak transcription	HepG2	liver
12	chr1:62757800-62760000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:62758400-62760000	Weak transcription	H1 Cell Line	embryonic stem cell

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