Variant report

Variant	rs219625
Chromosome Location	chr21:27864974-27864975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11088000	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs11088001	1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[ASN][1000 genomes]
rs170177	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs219632	0.83[YRI][hapmap]
rs219671	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs219672	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs222158	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs222159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs222160	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs222178	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs222971	0.84[CEU][hapmap]
rs2830249	0.83[YRI][hapmap]
rs2830250	0.86[ASN][1000 genomes]
rs2830251	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2830253	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs2830254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs701719	0.94[ASN][1000 genomes]

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	nsv1056506	chr21:27332898-28049880	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv544412	chr21:27332898-28049880	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv587335	chr21:27715263-27955385	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv913660	chr21:27815652-27869676	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv587336	chr21:27849346-27865978	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
6	esv1844181	chr21:27854701-27879342	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs219625	CCT8	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:27843400-27878800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr21:27852600-27867600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr21:27852800-27871400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr21:27862600-27878800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr21:27862800-27865200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr21:27863000-27865400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr21:27863400-27877600	Weak transcription	Fetal Lung	lung
8	chr21:27864200-27865600	Weak transcription	Fetal Kidney	kidney
9	chr21:27864200-27869600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr21:27864200-27872800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr21:27864400-27865400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr21:27864400-27870600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr21:27864400-27872600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr21:27864800-27894000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links