Variant report

Variant	rs7564579
Chromosome Location	chr2:39983431-39983432
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	chr2:39983322..39985987-chr2:40005030..40007807,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138050	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10168666	1.00[AMR][1000 genomes]
rs10171615	1.00[AMR][1000 genomes]
rs10177342	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10197101	0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12712654	0.94[YRI][hapmap];0.96[AFR][1000 genomes]
rs12712655	0.96[AFR][1000 genomes]
rs13393172	0.94[YRI][hapmap];0.96[AFR][1000 genomes]
rs13412186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13416764	1.00[AMR][1000 genomes]
rs28406334	0.86[AFR][1000 genomes]
rs57728145	0.83[AFR][1000 genomes]
rs59146573	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61706206	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544243	0.89[YRI][hapmap];0.89[AFR][1000 genomes]
rs6725034	0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6742533	0.94[YRI][hapmap]
rs6744797	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6749057	0.94[YRI][hapmap];0.93[AFR][1000 genomes]
rs6761738	0.83[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73924903	1.00[AMR][1000 genomes]
rs7603886	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv873890	chr2:39976810-40009041	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39960200-39987200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:39961400-39984200	Weak transcription	Colonic Mucosa	Colon
3	chr2:39962200-39986800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:39962200-39993200	Strong transcription	Liver	Liver
5	chr2:39964200-39984200	Weak transcription	Psoas Muscle	Psoas
6	chr2:39965200-40005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:39965200-40005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:39965400-39984200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:39967600-39991200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:39969800-39999800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:39971000-39999800	Weak transcription	Right Ventricle	heart
12	chr2:39971600-39998800	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr2:39972400-39998600	Strong transcription	HMEC	breast
14	chr2:39972400-39998800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:39973000-39998800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:39973600-39983600	Weak transcription	Pancreas	Pancrea
17	chr2:39974200-39998600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:39974600-39994000	Strong transcription	Fetal Thymus	thymus
19	chr2:39975000-39998400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:39975000-39999800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:39975200-39987200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:39975200-39987400	Strong transcription	Fetal Lung	lung
23	chr2:39975200-39987400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr2:39975200-39989000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr2:39975200-39989800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:39975200-39993800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr2:39975400-39987800	Strong transcription	Fetal Intestine Large	intestine
28	chr2:39975400-39997000	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:39975800-39985800	Strong transcription	Fetal Brain Female	brain
30	chr2:39975800-39989400	Strong transcription	A549	lung
31	chr2:39975800-39994600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:39976000-39988600	Strong transcription	HepG2	liver
33	chr2:39976000-39988800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr2:39976000-39989800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:39976000-39993200	Strong transcription	Placenta	Placenta
36	chr2:39976000-39993400	Strong transcription	Adipose Nuclei	Adipose
37	chr2:39976200-39987800	Strong transcription	Primary B cells from peripheral blood	blood
38	chr2:39976200-39987800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:39976200-39995400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:39976200-39998800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr2:39976400-39983600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:39976400-39992000	Strong transcription	K562	blood
43	chr2:39976600-39987200	Strong transcription	Primary hematopoietic stem cells	blood
44	chr2:39976600-39992000	Strong transcription	Primary B cells from cord blood	blood
45	chr2:39976800-39987600	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr2:39976800-39988800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr2:39976800-39999000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:39977000-39987600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:39977000-39990000	Strong transcription	Fetal Muscle Leg	muscle
50	chr2:39977200-39988000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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