Variant report

Variant	rs2809296
Chromosome Location	chr1:216560881-216560882
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10864238	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs10864239	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs11117565	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11117568	0.92[CEU][hapmap]
rs11120758	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs11120762	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs11590382	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs1339962	1.00[JPT][hapmap]
rs1339963	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1355630	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs1538691	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1588657	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2669053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2791292	0.96[CEU][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2809299	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs4078266	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4253963	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4323773	1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4396173	0.88[CHB][hapmap]
rs4488081	0.86[CEU][hapmap]
rs4531347	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4575147	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4846422	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4846428	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6604658	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs6660228	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs6664755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7518771	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521264	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7534756	0.85[ASN][1000 genomes]
rs7539376	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7539597	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs955942	1.00[CEU][hapmap];0.93[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]
rs974601	0.81[CHB][hapmap];1.00[JPT][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	nsv1006504	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv535288	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv549199	chr1:216384908-216814702	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1003815	chr1:216504235-216836498	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv535289	chr1:216504235-216836498	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv523863	chr1:216517635-216629416	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 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	chr1:216557200-216565000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:216560400-216561000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:216560400-216565400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:216560600-216563200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr1:216560600-216563800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:216560800-216561000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
7	chr1:216560800-216561400	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr1:216560800-216562600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr1:216560800-216563800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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