Variant report

Variant	rs11688838
Chromosome Location	chr2:142819607-142819608
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1001629	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10496914	0.85[CHB][hapmap]
rs10803487	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs10928133	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10928134	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11677754	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680286	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs11691560	0.85[CHB][hapmap]
rs11691595	0.85[CHB][hapmap]
rs11692364	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12105566	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12105584	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12470890	0.82[CHB][hapmap]
rs12618881	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12619411	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs12621782	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12998297	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13000270	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13036224	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1349219	0.82[CHB][hapmap]
rs1349221	0.82[CHB][hapmap]
rs1349222	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1375603	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1375609	0.85[CHB][hapmap]
rs1375612	0.84[CHB][hapmap]
rs1375613	0.81[CHB][hapmap]
rs1375616	0.91[ASN][1000 genomes]
rs1449475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1449476	0.81[CHB][hapmap]
rs1449477	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs1449478	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs1449480	0.81[CHB][hapmap]
rs1449481	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1449482	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs1449485	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1449489	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs1449490	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1449494	0.91[ASN][1000 genomes]
rs1449495	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1449496	0.91[ASN][1000 genomes]
rs1449498	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1449499	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1449501	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1449503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1449504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17824487	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1868542	0.82[CHB][hapmap]
rs1868543	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1868544	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1900933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1900934	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2029142	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2060592	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2167053	0.82[CHB][hapmap]
rs2197910	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2218734	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2381203	0.85[CHB][hapmap]
rs34392492	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4662219	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs4662370	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4662373	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62155598	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62157626	0.91[ASN][1000 genomes]
rs62157627	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6744928	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs6754907	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7558803	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7566250	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs7581031	0.82[CHB][hapmap]
rs7586417	0.80[ASN][1000 genomes]
rs7598886	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7608258	0.82[CHB][hapmap]
rs7609479	0.81[CHB][hapmap]
rs957376	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs993935	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9941495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941695	0.98[ASN][1000 genomes]
rs997123	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv530398	chr2:142474842-142843839	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv997274	chr2:142760393-143599193	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv526107	chr2:142768518-142884248	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv875253	chr2:142805006-142855291	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 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	chr2:142811600-142821400	Weak transcription	Brain Hippocampus Middle	brain
2	chr2:142818400-142821400	Weak transcription	Brain Angular Gyrus	brain
3	chr2:142819000-142819800	Enhancers	Brain Anterior Caudate	brain
4	chr2:142819000-142820000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:142819000-142820200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr2:142819000-142820200	Enhancers	Brain Substantia Nigra	brain
7	chr2:142819200-142819800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:142819400-142820200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:142819600-142820000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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