Variant report

Variant	rs2841540
Chromosome Location	chr6:13510618-13510619
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	chr6:13484853..13486653-chr6:13507774..13510681,2	MCF-7	breast:
3	chr6:13509236..13512148-chr6:13513623..13517377,3	K562	blood:
4	chr6:13486149..13488629-chr6:13509157..13510950,2	MCF-7	breast:
5	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: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs2494775	0.90[ASN][1000 genomes]
rs2560767	0.86[ASN][1000 genomes]
rs2560769	0.82[ASN][1000 genomes]
rs2560774	0.91[ASN][1000 genomes]
rs2560775	0.91[ASN][1000 genomes]
rs2560776	0.91[ASN][1000 genomes]
rs2560777	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2560778	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2560780	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2560781	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2560784	0.99[ASN][1000 genomes]
rs2560786	0.96[ASN][1000 genomes]
rs2560787	0.99[ASN][1000 genomes]
rs2560789	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560790	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560791	0.99[ASN][1000 genomes]
rs2560792	0.86[EUR][1000 genomes]
rs2560793	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560794	0.97[ASN][1000 genomes]
rs2560796	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560797	1.00[ASN][1000 genomes]
rs2560798	0.99[ASN][1000 genomes]
rs2560799	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2560800	0.90[ASN][1000 genomes]
rs2560802	0.98[ASN][1000 genomes]
rs2560803	0.88[ASN][1000 genomes]
rs2560804	0.98[ASN][1000 genomes]
rs2560805	0.98[ASN][1000 genomes]
rs2560806	0.98[ASN][1000 genomes]
rs2841526	0.91[ASN][1000 genomes]
rs2841527	0.91[ASN][1000 genomes]
rs2841528	0.91[ASN][1000 genomes]
rs2841530	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2841531	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2841532	0.99[ASN][1000 genomes]
rs2841533	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841535	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841536	0.97[ASN][1000 genomes]
rs2841537	0.98[ASN][1000 genomes]
rs2841539	0.84[ASN][1000 genomes]
rs2841542	0.98[ASN][1000 genomes]
rs2841543	0.98[ASN][1000 genomes]
rs2841544	0.98[ASN][1000 genomes]
rs2841545	0.98[ASN][1000 genomes]
rs4340988	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4512205	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4715370	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715371	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715372	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715373	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4715374	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4715375	0.82[EUR][1000 genomes]
rs4715376	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4715379	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4715380	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59610068	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60499941	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458898	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6923024	0.88[ASN][1000 genomes]
rs6939496	0.88[ASN][1000 genomes]
rs9367502	0.86[EUR][1000 genomes]
rs9370167	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370168	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370171	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370172	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9382154	0.86[EUR][1000 genomes]
rs9382156	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9382170	0.99[ASN][1000 genomes]
rs9382172	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382174	0.98[EUR][1000 genomes];0.97[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:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13500200-13512600	Weak transcription	Small Intestine	intestine
2	chr6:13506200-13512400	Weak transcription	Right Atrium	heart
3	chr6:13507000-13511200	Weak transcription	Spleen	Spleen
4	chr6:13507200-13512400	Weak transcription	Left Ventricle	heart
5	chr6:13509600-13511000	Weak transcription	Psoas Muscle	Psoas
6	chr6:13509600-13511800	Weak transcription	Fetal Stomach	stomach
7	chr6:13510000-13511000	Enhancers	Adipose Nuclei	Adipose
8	chr6:13510000-13513600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:13510200-13510800	Enhancers	Stomach Mucosa	stomach
10	chr6:13510200-13512000	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr6:13510200-13513600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:13510400-13511600	Weak transcription	Fetal Lung	lung
13	chr6:13510400-13511800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr6:13510400-13512000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:13510600-13511600	Weak transcription	Fetal Muscle Leg	muscle
16	chr6:13510600-13512000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:13510600-13512000	Weak transcription	NHLF	lung

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