Variant report

Variant	rs16886188
Chromosome Location	chr6:54781608-54781609
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:54560989..54563870-chr6:54779771..54781666,2	MCF-7	breast:
2	chr6:54709202..54711186-chr6:54779955..54782595,2	MCF-7	breast:
3	chr6:54562300..54564099-chr6:54779694..54781853,2	MCF-7	breast:
4	chr6:54775520..54777721-chr6:54779358..54781704,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs12055817	1.00[AFR][1000 genomes]
rs12175211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16886094	0.88[EUR][1000 genomes]
rs35576476	0.82[ASN][1000 genomes]
rs3813847	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4594937	0.82[ASN][1000 genomes]
rs62412651	0.88[EUR][1000 genomes]
rs62412652	0.83[EUR][1000 genomes]
rs62412655	0.88[EUR][1000 genomes]
rs62412657	0.88[EUR][1000 genomes]
rs62412658	0.88[EUR][1000 genomes]
rs62412659	0.88[EUR][1000 genomes]
rs62414961	0.81[ASN][1000 genomes]
rs62414962	0.94[EUR][1000 genomes]
rs62414963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62416361	1.00[AFR][1000 genomes]
rs62416376	1.00[AFR][1000 genomes]
rs62416516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62416519	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62416520	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62416521	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62416542	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71560884	0.87[ASN][1000 genomes]
rs9349746	0.82[ASN][1000 genomes]
rs9357821	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357824	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9357827	0.82[ASN][1000 genomes]
rs9357828	1.00[AFR][1000 genomes]
rs9357833	1.00[AFR][1000 genomes]
rs9357834	1.00[AFR][1000 genomes]
rs9367598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9367603	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9370338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9370339	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9370340	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9370341	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9370349	0.87[ASN][1000 genomes]
rs9370356	1.00[AFR][1000 genomes]
rs9370365	0.82[ASN][1000 genomes]
rs9370368	1.00[AFR][1000 genomes]
rs9370372	1.00[AFR][1000 genomes]
rs9382401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9382410	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9382412	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9382413	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9382423	0.82[ASN][1000 genomes]
rs9382424	0.82[ASN][1000 genomes]
rs9382433	1.00[AFR][1000 genomes]
rs9382435	1.00[AFR][1000 genomes]
rs9382439	1.00[AFR][1000 genomes]
rs9396026	1.00[AFR][1000 genomes]
rs9396029	0.82[ASN][1000 genomes]
rs9396030	0.82[ASN][1000 genomes]
rs980823	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54775600-54788400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:54776000-54796800	Weak transcription	Fetal Intestine Small	intestine
3	chr6:54778400-54785600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:54780800-54781800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:54780800-54782200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:54780800-54782200	Enhancers	NHEK	skin
7	chr6:54781200-54782200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:54781200-54782200	Enhancers	HMEC	breast
9	chr6:54781400-54781800	Enhancers	Duodenum Mucosa	Duodenum
10	chr6:54781400-54782000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:54781400-54782000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr6:54781400-54782200	Enhancers	Rectal Mucosa Donor 31	rectum

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