Variant report

Variant	rs2439559
Chromosome Location	chr6:13340811-13340812
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13327503..13331011-chr6:13335452..13341378,7	MCF-7	breast:
2	chr6:13339419..13342239-chr6:13348403..13350162,2	MCF-7	breast:
3	chr6:13338989..13341247-chr6:13343488..13345910,2	MCF-7	breast:
4	chr6:13340016..13342651-chr6:13343098..13344722,2	K562	blood:

Variant related genes	Relation type
ENSG00000145979	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10948641	1.00[EUR][1000 genomes]
rs11754614	1.00[EUR][1000 genomes]
rs11755431	1.00[EUR][1000 genomes]
rs11756770	1.00[EUR][1000 genomes]
rs11756942	1.00[EUR][1000 genomes]
rs11757262	1.00[EUR][1000 genomes]
rs11758235	1.00[EUR][1000 genomes]
rs11759443	1.00[EUR][1000 genomes]
rs16873780	1.00[EUR][1000 genomes]
rs2496171	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28495821	1.00[EUR][1000 genomes]
rs35114287	1.00[EUR][1000 genomes]
rs4452644	1.00[EUR][1000 genomes]
rs526661	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6911459	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6912427	1.00[EUR][1000 genomes]
rs6920849	1.00[EUR][1000 genomes]
rs6925659	1.00[EUR][1000 genomes]
rs73359121	1.00[EUR][1000 genomes]
rs754439	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7742713	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs878560	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9463696	1.00[EUR][1000 genomes]
rs9474025	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9474036	1.00[EUR][1000 genomes]
rs9474040	1.00[EUR][1000 genomes]
rs9474061	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13329400-13344200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:13335600-13341400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:13335600-13341800	Weak transcription	Right Atrium	heart
4	chr6:13336800-13341200	Enhancers	Primary B cells from cord blood	blood
5	chr6:13336800-13341600	Enhancers	Primary B cells from peripheral blood	blood
6	chr6:13337200-13351200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:13337400-13341800	Weak transcription	Left Ventricle	heart
8	chr6:13338800-13341200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr6:13340200-13341200	Enhancers	GM12878-XiMat	blood
10	chr6:13340400-13341000	Enhancers	Primary hematopoietic stem cells	blood
11	chr6:13340400-13341000	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr6:13340400-13341000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:13340400-13341000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:13340400-13341000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr6:13340600-13346000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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