Variant report

Variant	rs2560787
Chromosome Location	chr6:13509565-13509566
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13509314..13512710-chr6:13515099..13518078,3	MCF-7	breast:
2	chr6:13508787..13510378-chr6:13511004..13513571,2	K562	blood:
3	chr6:13484853..13486653-chr6:13507774..13510681,2	MCF-7	breast:
4	chr6:13509236..13512148-chr6:13513623..13517377,3	K562	blood:
5	chr6:13486149..13488629-chr6:13509157..13510950,2	MCF-7	breast:
6	chr6:13489525..13492132-chr6:13508702..13511366,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187461	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000145990	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs2494775	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2560764	0.84[EUR][1000 genomes]
rs2560767	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2560769	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2560774	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2560775	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2560776	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2560777	0.97[ASN][1000 genomes]
rs2560778	0.97[ASN][1000 genomes]
rs2560780	0.97[ASN][1000 genomes]
rs2560781	0.97[ASN][1000 genomes]
rs2560784	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560786	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2560789	0.99[ASN][1000 genomes]
rs2560790	0.99[ASN][1000 genomes]
rs2560791	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560793	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2560794	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2560796	0.99[ASN][1000 genomes]
rs2560797	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2560798	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2560799	0.96[ASN][1000 genomes]
rs2560800	0.89[ASN][1000 genomes]
rs2560802	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2560803	0.87[ASN][1000 genomes]
rs2560804	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2560805	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2560806	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2841504	0.84[EUR][1000 genomes]
rs2841526	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2841527	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2841528	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2841530	0.96[ASN][1000 genomes]
rs2841531	0.92[ASN][1000 genomes]
rs2841532	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841533	0.99[ASN][1000 genomes]
rs2841535	0.99[ASN][1000 genomes]
rs2841536	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2841537	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2841539	0.85[ASN][1000 genomes]
rs2841540	0.99[ASN][1000 genomes]
rs2841542	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2841543	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2841544	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2841545	0.97[ASN][1000 genomes]
rs2841572	0.83[EUR][1000 genomes]
rs4340988	0.97[ASN][1000 genomes]
rs4512205	0.97[ASN][1000 genomes]
rs4715370	0.99[ASN][1000 genomes]
rs4715371	0.99[ASN][1000 genomes]
rs4715372	0.99[ASN][1000 genomes]
rs4715373	0.97[ASN][1000 genomes]
rs4715374	0.97[ASN][1000 genomes]
rs4715376	0.92[ASN][1000 genomes]
rs4715379	0.91[ASN][1000 genomes]
rs4715380	0.91[ASN][1000 genomes]
rs59610068	0.99[ASN][1000 genomes]
rs60499941	0.99[ASN][1000 genomes]
rs62387368	0.81[EUR][1000 genomes]
rs62387369	0.81[EUR][1000 genomes]
rs6458898	0.93[ASN][1000 genomes]
rs6923024	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6939496	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9370167	0.99[ASN][1000 genomes]
rs9370168	0.99[ASN][1000 genomes]
rs9370171	0.99[ASN][1000 genomes]
rs9370172	0.98[ASN][1000 genomes]
rs9382156	0.97[ASN][1000 genomes]
rs9382170	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382172	0.99[ASN][1000 genomes]
rs9382174	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1033620	chr6:13419730-13571788	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv462640	chr6:13426539-13519434	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv600994	chr6:13426539-13519434	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv470802	chr6:13441424-13519371	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13500200-13512600	Weak transcription	Small Intestine	intestine
2	chr6:13506200-13509800	Weak transcription	Fetal Muscle Leg	muscle
3	chr6:13506200-13512400	Weak transcription	Right Atrium	heart
4	chr6:13507000-13511200	Weak transcription	Spleen	Spleen
5	chr6:13507200-13512400	Weak transcription	Left Ventricle	heart
6	chr6:13508600-13509600	Enhancers	Adipose Nuclei	Adipose
7	chr6:13508600-13509800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:13508600-13510000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:13508600-13510000	Enhancers	NHDF-Ad	bronchial
10	chr6:13508800-13509600	Enhancers	HSMMtube	muscle
11	chr6:13508800-13510400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr6:13508800-13510600	Enhancers	Stomach Smooth Muscle	stomach
13	chr6:13509000-13509600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:13509000-13509600	Enhancers	Fetal Stomach	stomach
15	chr6:13509000-13509600	Enhancers	Psoas Muscle	Psoas
16	chr6:13509000-13509600	Enhancers	GM12878-XiMat	blood
17	chr6:13509400-13509600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:13509400-13509800	Enhancers	Osteobl	bone
19	chr6:13509400-13510200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:13509400-13510400	Enhancers	Fetal Lung	lung
21	chr6:13509400-13510400	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr6:13509400-13510600	Enhancers	NHLF	lung

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