Variant report

Variant	rs2807988
Chromosome Location	chr10:22241212-22241213
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:22233292..22234846-chr10:22241021..22243031,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10508639	0.82[CEU][hapmap]
rs10740991	0.86[CEU][hapmap]
rs10740997	0.81[CEU][hapmap];0.84[AMR][1000 genomes]
rs10764330	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs10828266	0.85[CEU][hapmap]
rs10828283	0.86[EUR][1000 genomes]
rs1086896	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1086897	0.82[AMR][1000 genomes]
rs1086899	0.95[CEU][hapmap];0.84[AMR][1000 genomes]
rs11012794	0.84[CEU][hapmap]
rs11012840	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12571634	0.85[CEU][hapmap]
rs2066270	0.81[EUR][1000 genomes]
rs2066271	0.81[EUR][1000 genomes]
rs2252343	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2457954	0.89[CEU][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes]
rs2487512	0.95[CEU][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2666750	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2666753	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2666754	0.81[EUR][1000 genomes]
rs2666756	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2666757	0.81[EUR][1000 genomes]
rs2666759	0.81[CEU][hapmap]
rs2666760	1.00[CEU][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2666761	0.82[EUR][1000 genomes]
rs2666762	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2666763	0.80[EUR][1000 genomes]
rs2666768	0.82[CEU][hapmap]
rs2666771	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs2666775	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs2666776	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs2666779	0.81[EUR][1000 genomes]
rs2666781	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2666782	0.82[CEU][hapmap]
rs2793341	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2793351	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2793352	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2807966	0.81[EUR][1000 genomes]
rs2807968	0.81[EUR][1000 genomes]
rs2807971	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs2807978	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2807979	0.81[CEU][hapmap]
rs2807980	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2807982	0.86[CEU][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2807983	0.95[CEU][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2807984	0.81[CEU][hapmap]
rs2807987	0.81[CEU][hapmap]
rs2859622	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs2941733	0.81[EUR][1000 genomes]
rs4024198	0.81[CEU][hapmap]
rs4146689	0.81[CEU][hapmap]
rs4748775	0.81[EUR][1000 genomes]
rs4748777	0.80[EUR][1000 genomes]
rs4748778	0.80[EUR][1000 genomes]
rs4748779	0.81[CEU][hapmap]
rs6650129	0.90[CEU][hapmap];0.84[AMR][1000 genomes]
rs6650130	0.86[CEU][hapmap];0.84[AMR][1000 genomes]
rs7089656	0.81[CEU][hapmap]
rs7904395	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7910002	0.95[CEU][hapmap]
rs792455	0.81[EUR][1000 genomes]
rs792456	0.83[EUR][1000 genomes]
rs792457	0.82[AMR][1000 genomes]
rs792458	0.86[EUR][1000 genomes]
rs806774	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1802317	chr10:21866085-22288132	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv1793816	chr10:22088054-22285371	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1048924	chr10:22177164-22296409	Enhancers Bivalent/Poised TSS Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv831808	chr10:22187850-22357814	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv894948	chr10:22203392-22255097	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1795981	chr10:22223984-22253054	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2807988	MLLT10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:22199600-22250800	Weak transcription	Pancreas	Pancrea
2	chr10:22232800-22243000	Weak transcription	Primary B cells from cord blood	blood
3	chr10:22233000-22242600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr10:22233000-22243000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr10:22233600-22242600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr10:22233800-22245000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr10:22237200-22250800	Weak transcription	Left Ventricle	heart
8	chr10:22238000-22242400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr10:22238200-22250400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr10:22239800-22241400	Weak transcription	Psoas Muscle	Psoas
11	chr10:22239800-22242800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr10:22240800-22241400	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr10:22240800-22244200	Enhancers	GM12878-XiMat	blood
14	chr10:22241000-22241600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr10:22241000-22241600	Enhancers	A549	lung
16	chr10:22241200-22241800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links