Variant report

Variant	rs981682
Chromosome Location	chr6:54583335-54583336
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:54574954..54578587-chr6:54580352..54583856,5	MCF-7	breast:
2	chr6:54578251..54580318-chr6:54581650..54584206,2	MCF-7	breast:
3	chr6:54568299..54570747-chr6:54582453..54584898,3	MCF-7	breast:
4	chr6:54581649..54583716-chr6:54731091..54732634,2	MCF-7	breast:
5	chr6:54561293..54570100-chr6:54582505..54590247,14	MCF-7	breast:
6	chr6:54574192..54576279-chr6:54583056..54585185,2	MCF-7	breast:
7	chr6:54580831..54596896-chr6:54704751..54716103,89	MCF-7	breast:
8	chr6:54582146..54584053-chr6:54741073..54743084,2	MCF-7	breast:
9	chr6:54582065..54584949-chr6:54722187..54724387,3	MCF-7	breast:
10	chr6:54577593..54590845-chr6:54708062..54715554,67	MCF-7	breast:
11	chr6:54581970..54584648-chr6:54584800..54586441,2	MCF-7	breast:
12	chr6:54582003..54585202-chr6:54737626..54739872,3	MCF-7	breast:
13	chr6:54582713..54585752-chr6:54741876..54745709,4	MCF-7	breast:
14	chr6:54582865..54585119-chr6:54718425..54721186,2	MCF-7	breast:
15	chr6:54559803..54567776-chr6:54579525..54585377,11	MCF-7	breast:
16	chr6:54582596..54584566-chr6:55092481..55094780,2	MCF-7	breast:
17	chr6:54581587..54585941-chr6:54586924..54591451,7	MCF-7	breast:
18	chr6:54570566..54573467-chr6:54582462..54585489,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction
ENSG00000224984	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1039693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13193002	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs13217514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1911508	0.81[ASN][1000 genomes]
rs2174145	0.82[CEU][hapmap]
rs2297804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6459021	0.85[CEU][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6899853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908136	0.81[ASN][1000 genomes]
rs6914808	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6916681	0.81[CEU][hapmap]
rs6929108	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs925057	0.80[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs9464124	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9474965	0.80[ASN][1000 genomes]
rs9474972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9474973	0.81[ASN][1000 genomes]
rs9474974	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474991	0.86[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap]
rs995951	0.82[JPT][hapmap];0.81[ASN][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:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54582400-54583800	Enhancers	NHEK	skin
2	chr6:54582400-54585000	Enhancers	Fetal Lung	lung
3	chr6:54582600-54583800	Enhancers	Stomach Mucosa	stomach
4	chr6:54582800-54584200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:54583000-54583400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr6:54583000-54583400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:54583000-54583400	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr6:54583000-54583400	Flanking Active TSS	Fetal Intestine Small	intestine
9	chr6:54583000-54583400	Weak transcription	Fetal Kidney	kidney
10	chr6:54583000-54583400	Active TSS	HMEC	breast
11	chr6:54583000-54583600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:54583000-54583800	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr6:54583000-54584000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:54583000-54584000	Enhancers	Fetal Intestine Large	intestine
15	chr6:54583000-54584000	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr6:54583000-54584200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:54583000-54584200	Active TSS	Duodenum Mucosa	Duodenum
18	chr6:54583000-54584600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr6:54583000-54584600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:54583000-54584600	Enhancers	Fetal Brain Female	brain
21	chr6:54583000-54584800	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr6:54583200-54583400	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr6:54583200-54583400	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr6:54583200-54583800	Enhancers	Fetal Stomach	stomach
25	chr6:54583200-54584000	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr6:54583200-54585400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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