Variant report

Variant	rs16887169
Chromosome Location	chr6:55652400-55652401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10948957	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs12174118	0.91[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs3798834	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs3823040	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs9296801	0.91[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs9296802	0.91[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs9349795	0.91[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs9349796	0.91[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs9367666	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9370468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9382559	0.82[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs9396156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1026411	chr6:55372845-55653498	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv885909	chr6:55539010-55674338	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1019228	chr6:55608688-55653498	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv2752670	chr6:55614978-55781605	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv885910	chr6:55628283-55684300	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv603164	chr6:55631762-55674338	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55618200-55672400	Weak transcription	Placenta	Placenta
2	chr6:55641000-55653200	Weak transcription	Fetal Heart	heart
3	chr6:55643000-55655000	Weak transcription	Fetal Lung	lung
4	chr6:55643200-55659000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:55648200-55657400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:55648400-55658000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:55651800-55652800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:55651800-55654800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:55652000-55653000	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr6:55652200-55652600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr6:55652200-55652600	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr6:55652200-55652600	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr6:55652400-55652600	Enhancers	Hela-S3	cervix

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