Variant report

Variant	rs6040436
Chromosome Location	chr20:11200008-11200009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:10652777..10656154-chr20:11197961..11200828,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270792	Chromatin interaction
ENSG00000101384	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1473701	0.84[EUR][1000 genomes]
rs1473702	0.84[EUR][1000 genomes]
rs1473703	0.81[EUR][1000 genomes]
rs2015108	0.88[EUR][1000 genomes]
rs2076646	0.88[EUR][1000 genomes]
rs2076647	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2143857	0.88[EUR][1000 genomes]
rs2179827	0.86[EUR][1000 genomes]
rs2207098	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2207099	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2207100	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4643605	0.81[EUR][1000 genomes]
rs4813966	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4813967	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4813968	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4813969	0.83[EUR][1000 genomes]
rs4813971	0.84[EUR][1000 genomes]
rs6033062	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6033063	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6033068	0.81[EUR][1000 genomes]
rs6040435	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6040442	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6040446	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6040447	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6040450	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6040451	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6040452	0.88[EUR][1000 genomes]
rs6040456	0.88[EUR][1000 genomes]
rs6040460	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6040464	0.83[EUR][1000 genomes]
rs6040465	0.83[EUR][1000 genomes]
rs6040466	0.83[EUR][1000 genomes]
rs6040469	0.83[EUR][1000 genomes]
rs6040471	0.83[EUR][1000 genomes]
rs6040480	0.83[EUR][1000 genomes]
rs6040481	0.80[EUR][1000 genomes]
rs6078109	0.82[EUR][1000 genomes]
rs6104726	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6108864	0.82[CHB][hapmap]
rs6108870	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6108871	0.88[EUR][1000 genomes]
rs6108872	0.88[EUR][1000 genomes]
rs714690	0.88[EUR][1000 genomes]
rs714691	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs714692	0.88[EUR][1000 genomes]
rs761471	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs761472	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs926725	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs983251	0.88[EUR][1000 genomes]
rs983252	0.88[EUR][1000 genomes]
rs983342	0.88[EUR][1000 genomes]
rs983343	0.88[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	nsv1065969	chr20:10850562-11464172	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv544181	chr20:10850562-11464172	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv585415	chr20:11134907-11383327	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1056067	chr20:11174581-11213919	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 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	chr20:11195200-11201800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr20:11195600-11210200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr20:11197000-11200200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr20:11197600-11200600	Enhancers	Primary B cells from cord blood	blood
5	chr20:11197800-11200200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr20:11197800-11201600	Enhancers	Fetal Heart	heart
7	chr20:11198000-11201400	Weak transcription	Brain Hippocampus Middle	brain
8	chr20:11198400-11200800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr20:11198400-11201400	Weak transcription	Ovary	ovary
10	chr20:11198400-11202800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr20:11198400-11209200	Weak transcription	Aorta	Aorta
12	chr20:11199000-11201400	Enhancers	GM12878-XiMat	blood
13	chr20:11199400-11201600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr20:11199600-11202000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr20:11199800-11201800	Weak transcription	Right Atrium	heart
16	chr20:11199800-11202800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr20:11200000-11200400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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