Variant report

Variant	rs12527124
Chromosome Location	chr6:54584345-54584346
allele	A/C
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:54583583..54586469-chr6:54727325..54729845,2	MCF-7	breast:
2	chr6:54583465..54585924-chr6:54724133..54726618,2	MCF-7	breast:
3	chr6:54568299..54570747-chr6:54582453..54584898,3	MCF-7	breast:
4	chr6:54561293..54570100-chr6:54582505..54590247,14	MCF-7	breast:
5	chr6:54574192..54576279-chr6:54583056..54585185,2	MCF-7	breast:
6	chr6:54580831..54596896-chr6:54704751..54716103,89	MCF-7	breast:
7	chr6:54582065..54584949-chr6:54722187..54724387,3	MCF-7	breast:
8	chr6:54577593..54590845-chr6:54708062..54715554,67	MCF-7	breast:
9	chr6:54581970..54584648-chr6:54584800..54586441,2	MCF-7	breast:
10	chr6:54582003..54585202-chr6:54737626..54739872,3	MCF-7	breast:
11	chr6:54582713..54585752-chr6:54741876..54745709,4	MCF-7	breast:
12	chr6:54582865..54585119-chr6:54718425..54721186,2	MCF-7	breast:
13	chr6:54559803..54567776-chr6:54579525..54585377,11	MCF-7	breast:
14	chr6:54582596..54584566-chr6:55092481..55094780,2	MCF-7	breast:
15	chr6:54581587..54585941-chr6:54586924..54591451,7	MCF-7	breast:
16	chr6:54570566..54573467-chr6:54582462..54585489,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000224984	Chromatin interaction
ENSG00000168143	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1039495	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1039496	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10948840	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10948844	0.95[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10948846	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11967781	0.85[CHB][hapmap]
rs12525001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12525539	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12527042	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12527077	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12527080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12528270	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12528881	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529275	0.90[EUR][1000 genomes]
rs12661998	0.96[ASN][1000 genomes]
rs12662465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395624	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1572593	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1648201	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16869519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16885649	0.90[EUR][1000 genomes]
rs16885656	0.90[EUR][1000 genomes]
rs16885668	0.90[EUR][1000 genomes]
rs16885735	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16885866	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16885911	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16885948	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1948954	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs1951693	0.80[EUR][1000 genomes]
rs1976539	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1983140	0.84[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs2048112	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048113	0.86[ASN][1000 genomes]
rs2894821	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34752465	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35953958	0.94[ASN][1000 genomes]
rs4712068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712070	0.87[CHB][hapmap]
rs4715468	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4715470	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4715478	0.95[ASN][1000 genomes]
rs4994100	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58302712	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60501416	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs608873	0.90[EUR][1000 genomes]
rs6459019	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67799698	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs67875074	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6915244	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73442093	0.86[ASN][1000 genomes]
rs73444113	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73444116	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73444125	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73446026	0.96[ASN][1000 genomes]
rs73446030	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73446036	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73446043	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7751908	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7761021	0.90[EUR][1000 genomes]
rs9349726	0.90[EUR][1000 genomes]
rs9370323	0.80[EUR][1000 genomes]
rs9474957	0.83[EUR][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	esv2654510	chr6:54583570-54585063	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54582400-54585000	Enhancers	Fetal Lung	lung
2	chr6:54583000-54584600	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr6:54583000-54584600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:54583000-54584600	Enhancers	Fetal Brain Female	brain
5	chr6:54583000-54584800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr6:54583200-54585400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:54583400-54584800	Enhancers	Fetal Kidney	kidney
8	chr6:54583400-54585000	Enhancers	Fetal Intestine Small	intestine
9	chr6:54583400-54585200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:54583600-54594200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:54583800-54584600	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr6:54583800-54584800	Weak transcription	Stomach Mucosa	stomach
13	chr6:54583800-54585800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:54583800-54586600	Weak transcription	NHEK	skin
15	chr6:54584000-54584600	Enhancers	HMEC	breast
16	chr6:54584000-54585200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:54584000-54585800	Weak transcription	Fetal Intestine Large	intestine
18	chr6:54584000-54586600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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