Variant report

Variant	rs12216049
Chromosome Location	chr6:54709969-54709970
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:54483454..54486448-chr6:54709404..54710933,2	MCF-7	breast:
2	chr6:54709139..54711220-chr6:54750997..54752618,2	MCF-7	breast:
3	chr20:52738859..52741782-chr6:54708785..54710307,2	MCF-7	breast:
4	chr6:54556132..54558033-chr6:54708676..54711461,2	MCF-7	breast:
5	chr6:54709202..54711186-chr6:54779955..54782595,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10807484	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10807485	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10948862	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10948864	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12191299	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12191386	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12194667	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12195438	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12196314	0.85[ASN][1000 genomes]
rs12201892	0.84[ASN][1000 genomes]
rs12202062	0.84[ASN][1000 genomes]
rs12203709	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12205222	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12205372	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12207559	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393778	0.84[AMR][1000 genomes]
rs1393779	0.88[AMR][1000 genomes]
rs1910357	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2270989	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs34713378	0.84[ASN][1000 genomes]
rs4712075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62412605	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6908745	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72957572	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7747352	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7760490	0.85[ASN][1000 genomes]
rs9296769	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9464148	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9464149	0.98[ASN][1000 genomes]
rs9475029	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9475038	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9475039	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9475040	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9475041	0.98[ASN][1000 genomes]
rs9475045	0.88[ASN][1000 genomes]
rs9475046	0.98[ASN][1000 genomes]

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	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
3	nsv823700	chr6:54709648-54710116	Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 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	chr6:54707200-54710800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:54707400-54710200	Weak transcription	NHEK	skin
3	chr6:54707400-54710800	Weak transcription	Placenta	Placenta
4	chr6:54709000-54710000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:54709000-54710400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:54709000-54713400	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr6:54709000-54714200	Active TSS	Duodenum Mucosa	Duodenum
8	chr6:54709200-54710200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:54709200-54710200	Enhancers	HMEC	breast
10	chr6:54709400-54710800	Weak transcription	Fetal Intestine Small	intestine
11	chr6:54709800-54710400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:54709800-54713400	Active TSS	Rectal Mucosa Donor 31	rectum

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