Variant report

Variant	rs3938656
Chromosome Location	chr6:77586771-77586772
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:76985498..76986021-chr6:77586428..77587326,2	MCF-7	breast:
2	chr6:77584071..77587000-chr6:77595332..77597359,2	MCF-7	breast:
3	chr6:77586174..77588444-chr6:77591839..77593898,2	MCF-7	breast:
4	chr6:77406988..77407870-chr6:77586545..77587424,2	MCF-7	breast:
5	chr6:77576372..77578055-chr6:77585429..77587014,2	MCF-7	breast:
6	chr6:77392645..77395103-chr6:77585280..77587587,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10214820	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10214846	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1582076	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1582077	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2105052	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4279388	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4318832	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4318833	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4557476	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6906837	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6913759	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6915450	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6929543	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6933472	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6938725	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6938815	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6939746	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6940241	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6940780	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9294034	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9294035	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9294036	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9294037	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9294038	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9294039	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9443298	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9443299	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9443300	0.94[AFR][1000 genomes]
rs9443301	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9443302	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9443303	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9443304	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9443305	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9447839	0.91[AFR][1000 genomes]
rs9447841	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9447842	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9447843	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9447845	0.90[AMR][1000 genomes]
rs9447857	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9447859	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9447860	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9447861	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9447862	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9447864	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9447867	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9447868	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9447869	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9447870	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9447872	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9447873	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9447875	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9447876	0.96[AFR][1000 genomes];1.00[AMR][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	nsv1019520	chr6:77355212-77875164	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv538321	chr6:77355212-77875164	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv830701	chr6:77509152-77678602	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv432924	chr6:77566201-77617213	Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
5	esv3387181	chr6:77571282-77594741	Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
6	nsv886222	chr6:77577055-77734250	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
7	nsv1017082	chr6:77585310-78258237	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:77585400-77590800	Weak transcription	Pancreas	Pancrea
2	chr6:77586200-77586800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:77586200-77586800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:77586200-77587000	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:77586200-77587000	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:77586200-77587000	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:77586200-77587000	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr6:77586400-77586800	Active TSS	H1 Cell Line	embryonic stem cell
9	chr6:77586400-77586800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:77586600-77587000	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr6:77586600-77587000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr6:77586600-77587200	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr6:77586600-77587200	Enhancers	Rectal Mucosa Donor 31	rectum

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