Variant report

Variant	rs16885860
Chromosome Location	chr6:54564231-54564232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:54558970..54566519-chr6:54708534..54713743,16	MCF-7	breast:
2	chr6:54563782..54566701-chr6:54762502..54764565,2	MCF-7	breast:
3	chr6:54551257..54553977-chr6:54562035..54564580,2	MCF-7	breast:
4	chr6:54562484..54564963-chr6:54735331..54738094,2	MCF-7	breast:
5	chr6:54559522..54567174-chr6:54707552..54714330,37	MCF-7	breast:
6	chr6:54485033..54487186-chr6:54562620..54564688,2	MCF-7	breast:
7	chr6:54561977..54564257-chr6:54570191..54572297,2	MCF-7	breast:
8	chr6:54564170..54566593-chr6:54739128..54740974,2	MCF-7	breast:
9	chr6:54560120..54562700-chr6:54564068..54565878,2	MCF-7	breast:
10	chr6:54561293..54570100-chr6:54582505..54590247,14	MCF-7	breast:
11	chr6:54559803..54567776-chr6:54579525..54585377,11	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs16885898	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56762989	1.00[AMR][1000 genomes]
rs61162376	1.00[AMR][1000 genomes]
rs62414312	0.90[AFR][1000 genomes]
rs6909009	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6909061	1.00[AMR][1000 genomes]
rs6933826	1.00[AMR][1000 genomes]
rs73741511	1.00[AMR][1000 genomes]
rs73743467	1.00[AMR][1000 genomes]
rs7758802	1.00[AMR][1000 genomes]
rs7776195	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54562400-54565400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr6:54562600-54565400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:54563400-54565000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:54563600-54564400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:54563600-54564600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:54563800-54564400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:54563800-54564400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:54563800-54564600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr6:54563800-54565200	Enhancers	Fetal Intestine Small	intestine
10	chr6:54564000-54564400	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr6:54564000-54564400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:54564000-54564400	Enhancers	Stomach Mucosa	stomach
13	chr6:54564000-54564400	Active TSS	HMEC	breast
14	chr6:54564200-54564400	Enhancers	Fetal Lung	lung
15	chr6:54564200-54565000	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr6:54564200-54565200	Flanking Active TSS	NHEK	skin
17	chr6:54564200-54571000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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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

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