Variant report

Variant	rs5990
Chromosome Location	chr1:197008597-197008598
allele	G/T
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:55)

rs_ID	r²[population]
rs10484502	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737685	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10754209	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10754216	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10801575	0.81[JPT][hapmap]
rs10801589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10801594	0.93[YRI][hapmap]
rs10922163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1127661	0.82[JPT][hapmap]
rs11589158	0.81[ASN][1000 genomes]
rs1170879	0.85[ASN][1000 genomes]
rs12755054	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1332661	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1332667	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1412635	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1611982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1615413	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1750311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17514309	0.85[ASN][1000 genomes]
rs17514324	0.86[ASN][1000 genomes]
rs17549312	0.83[ASN][1000 genomes]
rs17549360	0.86[ASN][1000 genomes]
rs17549430	0.86[ASN][1000 genomes]
rs1759016	0.93[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs17662710	0.91[ASN][1000 genomes]
rs1794011	0.83[ASN][1000 genomes]
rs2225565	0.89[ASN][1000 genomes]
rs2298882	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2336596	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2878749	0.82[JPT][hapmap]
rs3737111	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3748557	0.82[JPT][hapmap]
rs4244139	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[EUR][1000 genomes]
rs45445493	0.86[ASN][1000 genomes]
rs5996	0.85[ASN][1000 genomes]
rs5998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61820789	0.89[ASN][1000 genomes]
rs61820800	0.91[ASN][1000 genomes]
rs6677930	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs6700180	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6702252	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs698859	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs72736469	0.81[ASN][1000 genomes]
rs72736474	0.81[ASN][1000 genomes]
rs7410943	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs7514071	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7517428	0.86[ASN][1000 genomes]
rs7518773	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7525490	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7535993	0.95[ASN][1000 genomes]
rs857018	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs857024	0.91[ASN][1000 genomes]
rs857025	0.86[ASN][1000 genomes]
rs9427664	0.93[ASN][1000 genomes]
rs9727516	0.83[JPT][hapmap]

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	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758990	chr1:196590837-197169772	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv427897	chr1:196590837-197169772	Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv2756880	chr1:196709223-197066074	ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	esv34978	chr1:196733133-197011577	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv430158	chr1:196733133-197011577	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	esv2757767	chr1:196977799-197169772	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv947216	chr1:197003904-197019809	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	n/a
9	nsv873063	chr1:197007479-197025431	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	n/a
10	nsv873064	chr1:197008597-197035538	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197004800-197010600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:197005000-197012000	Weak transcription	A549	lung
3	chr1:197008200-197011400	Strong transcription	Liver	Liver

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