Variant report

Variant	rs2560789
Chromosome Location	chr6:13506906-13506907
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13486342..13488490-chr6:13504374..13507205,2	MCF-7	breast:
2	chr6:13486350..13490681-chr6:13504668..13507736,4	K562	blood:
3	chr6:13503277..13504938-chr6:13505521..13507595,2	K562	blood:

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

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs2081874	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs2494775	0.86[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs2560767	0.86[ASN][1000 genomes]
rs2560769	0.82[ASN][1000 genomes]
rs2560774	0.91[ASN][1000 genomes]
rs2560775	0.86[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2560776	0.86[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];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	0.87[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]
rs2560790	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];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	0.81[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[ASN][1000 genomes]
rs2560806	0.98[ASN][1000 genomes]
rs2841526	0.91[ASN][1000 genomes]
rs2841527	0.91[ASN][1000 genomes]
rs2841528	0.86[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];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	0.87[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]
rs2841540	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841542	0.98[ASN][1000 genomes]
rs2841543	0.81[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[ASN][1000 genomes]
rs2841544	0.81[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[ASN][1000 genomes]
rs2841545	0.98[ASN][1000 genomes]
rs2841548	0.85[CEU][hapmap];0.93[GIH][hapmap]
rs2841549	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs2841569	0.86[CHB][hapmap];0.94[JPT][hapmap]
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	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];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	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];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]
rs9382144	0.85[CEU][hapmap]
rs9382154	0.92[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];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:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13500200-13512600	Weak transcription	Small Intestine	intestine
2	chr6:13505600-13507600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:13505800-13507000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:13506000-13508600	Weak transcription	Adipose Nuclei	Adipose
5	chr6:13506000-13509400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr6:13506200-13508800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:13506200-13509800	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:13506200-13512400	Weak transcription	Right Atrium	heart
9	chr6:13506600-13507200	Enhancers	Left Ventricle	heart
10	chr6:13506800-13507000	Enhancers	Spleen	Spleen
11	chr6:13506800-13508000	Enhancers	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links