Variant report

Variant	rs239043
Chromosome Location	chr21:17557780-17557781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10854413	0.82[CEU][hapmap]
rs171190	1.00[CEU][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239036	1.00[MEX][hapmap];0.87[TSI][hapmap]
rs239041	1.00[ASN][1000 genomes]
rs239042	1.00[ASN][1000 genomes]
rs239044	1.00[ASW][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823625	0.87[TSI][hapmap]
rs2823626	1.00[MEX][hapmap];0.87[TSI][hapmap]
rs2823628	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2848688	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6517692	1.00[CHD][hapmap]
rs7277989	0.90[EUR][1000 genomes]
rs7282315	0.82[CEU][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs7283583	0.82[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066951	chr21:17458978-17603160	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv544381	chr21:17458978-17603160	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1065028	chr21:17522588-17572535	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17553200-17557800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr21:17553400-17559800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr21:17553400-17566400	Weak transcription	Fetal Stomach	stomach
4	chr21:17553800-17558000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr21:17555800-17558800	Weak transcription	Right Atrium	heart
6	chr21:17556200-17560400	Enhancers	Brain Cingulate Gyrus	brain
7	chr21:17556400-17559400	Weak transcription	Hela-S3	cervix
8	chr21:17556400-17559600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr21:17556600-17559200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr21:17556800-17559000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr21:17556800-17559200	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr21:17557000-17558400	Enhancers	Brain Anterior Caudate	brain
13	chr21:17557200-17559200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr21:17557200-17559200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr21:17557200-17559400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr21:17557200-17559800	Enhancers	Brain Substantia Nigra	brain
17	chr21:17557200-17560400	Enhancers	Brain Hippocampus Middle	brain
18	chr21:17557400-17558200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr21:17557400-17558400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr21:17557400-17559600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr21:17557400-17559600	Enhancers	Brain Angular Gyrus	brain
22	chr21:17557600-17558000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr21:17557600-17558200	Weak transcription	Ovary	ovary

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