Variant report

Variant	rs1402996
Chromosome Location	chr2:209849299-209849300
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10167720	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10178837	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10186320	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10192840	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10497912	0.93[EUR][1000 genomes]
rs10497913	0.94[EUR][1000 genomes]
rs10497914	0.94[EUR][1000 genomes]
rs10497915	0.95[CEU][hapmap];0.83[CHB][hapmap];0.94[EUR][1000 genomes]
rs10497916	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[EUR][1000 genomes]
rs10497917	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[EUR][1000 genomes]
rs1107012	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[EUR][1000 genomes]
rs11884061	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11884074	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12464172	0.94[EUR][1000 genomes]
rs12991020	0.94[EUR][1000 genomes]
rs13007238	0.92[EUR][1000 genomes]
rs13018777	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13019486	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13021774	0.92[EUR][1000 genomes]
rs13022155	0.94[EUR][1000 genomes]
rs13024347	0.94[EUR][1000 genomes]
rs13025032	0.94[EUR][1000 genomes]
rs13025499	0.95[EUR][1000 genomes]
rs13026927	0.88[EUR][1000 genomes]
rs13029761	0.94[EUR][1000 genomes]
rs13411078	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1357247	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1357248	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1402999	0.94[EUR][1000 genomes]
rs1522201	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1522202	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16842022	0.94[EUR][1000 genomes]
rs16842024	0.94[EUR][1000 genomes]
rs16842028	0.94[EUR][1000 genomes]
rs16842029	0.94[EUR][1000 genomes]
rs16842030	0.94[EUR][1000 genomes]
rs16842036	0.94[EUR][1000 genomes]
rs16842052	0.94[EUR][1000 genomes]
rs16842053	0.94[EUR][1000 genomes]
rs16842199	0.95[EUR][1000 genomes]
rs16842268	0.93[EUR][1000 genomes]
rs16842299	0.90[EUR][1000 genomes]
rs1818784	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1829708	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1851368	0.94[EUR][1000 genomes]
rs1949689	0.93[EUR][1000 genomes]
rs1969381	0.92[EUR][1000 genomes]
rs2364697	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2886146	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2886148	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34227926	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34326398	0.99[EUR][1000 genomes]
rs34578232	0.94[EUR][1000 genomes]
rs35179183	0.94[EUR][1000 genomes]
rs35245441	0.94[EUR][1000 genomes]
rs35251783	0.94[EUR][1000 genomes]
rs3851939	0.94[EUR][1000 genomes]
rs3851940	0.94[EUR][1000 genomes]
rs3851941	0.94[EUR][1000 genomes]
rs3863854	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3914935	0.93[EUR][1000 genomes]
rs3914937	0.94[EUR][1000 genomes]
rs4109419	0.94[EUR][1000 genomes]
rs4366838	0.94[EUR][1000 genomes]
rs5002645	0.94[EUR][1000 genomes]
rs56335750	0.93[EUR][1000 genomes]
rs58821250	0.92[EUR][1000 genomes]
rs66515766	0.94[EUR][1000 genomes]
rs6717179	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71409838	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72989312	0.89[EUR][1000 genomes]
rs73064322	0.94[EUR][1000 genomes]
rs7559978	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7580198	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7588985	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7599045	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7606381	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs883049	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs939848	0.96[EUR][1000 genomes]
rs9646841	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9989816	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460058	chr2:209755059-209866395	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv584306	chr2:209755059-209866395	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1012184	chr2:209755847-210049331	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv536131	chr2:209755847-210049331	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3487576	chr2:209768379-209947296	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3487577	chr2:209768379-209947296	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1009924	chr2:209805661-210042572	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv875760	chr2:209817526-209929978	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv1002578	chr2:209836205-210026339	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv536132	chr2:209836205-210026339	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209843000-209853600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:209847000-209850000	Enhancers	NHEK	skin
3	chr2:209847200-209849800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:209847800-209849800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:209848000-209851000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:209848600-209850200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:209849000-209849800	Enhancers	Placenta	Placenta
8	chr2:209849000-209849800	Enhancers	HMEC	breast
9	chr2:209849000-209850600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:209849200-209849400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:209849200-209849800	Enhancers	Pancreas	Pancrea

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