Variant report

Variant	rs2439590
Chromosome Location	chr5:112079857-112079858
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112078508..112080927-chr5:112081465..112083694,2	MCF-7	breast:
2	chr5:112042040..112044749-chr5:112077105..112080754,4	K562	blood:
3	chr5:112070264..112074990-chr5:112075213..112080518,8	K562	blood:
4	chr5:112036075..112039383-chr5:112077944..112080401,3	K562	blood:
5	chr5:112070801..112074184-chr5:112077517..112081527,4	K562	blood:

Variant related genes	Relation type
ENSG00000134982	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11953943	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs11960216	0.93[EUR][1000 genomes]
rs1644241	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1644242	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1661032	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1661034	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1697914	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1697916	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17134960	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs1734244	0.91[EUR][1000 genomes]
rs1734245	0.82[CEU][hapmap]
rs1734246	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1734247	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1882619	0.82[AMR][1000 genomes]
rs2431505	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2431507	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2431508	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2431509	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2431511	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2439592	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2439593	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2439594	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2455294	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2455296	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2464802	0.83[EUR][1000 genomes]
rs2464808	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2464810	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2909784	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2909961	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2909962	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs73220022	0.80[EUR][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	nsv830450	chr5:111964170-112134510	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv462387	chr5:112053911-112124369	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv599393	chr5:112053911-112124369	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv1032464	chr5:112076061-112192380	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv537862	chr5:112076061-112192380	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112073800-112086800	Weak transcription	Gastric	stomach
2	chr5:112074000-112095000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr5:112074200-112081400	Weak transcription	Esophagus	oesophagus
4	chr5:112074200-112083800	Weak transcription	Ovary	ovary
5	chr5:112074200-112084400	Weak transcription	Pancreas	Pancrea
6	chr5:112074200-112093200	Weak transcription	Aorta	Aorta
7	chr5:112074400-112081400	Weak transcription	Right Atrium	heart
8	chr5:112074400-112083800	Weak transcription	Psoas Muscle	Psoas
9	chr5:112074400-112083800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:112074400-112090400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr5:112074400-112090400	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr5:112074400-112091000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:112074400-112093200	Weak transcription	Right Ventricle	heart
14	chr5:112074400-112094000	Weak transcription	Fetal Intestine Small	intestine
15	chr5:112074400-112095200	Weak transcription	Fetal Muscle Leg	muscle
16	chr5:112074400-112095600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr5:112074400-112095600	Weak transcription	Fetal Thymus	thymus
18	chr5:112074400-112095800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr5:112074400-112102800	Weak transcription	Fetal Stomach	stomach
20	chr5:112074400-112103400	Weak transcription	Left Ventricle	heart
21	chr5:112074400-112119800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:112074400-112125600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:112074400-112128600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:112074600-112090400	Weak transcription	Primary B cells from cord blood	blood
25	chr5:112074600-112103000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:112074800-112097600	Weak transcription	HMEC	breast
27	chr5:112075000-112093000	Weak transcription	Liver	Liver
28	chr5:112075000-112095200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:112075200-112092600	Weak transcription	HSMM	muscle
30	chr5:112075200-112094400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:112075200-112103000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:112075400-112091000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr5:112075400-112097400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:112075400-112101600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr5:112075600-112095600	Weak transcription	Dnd41	blood
36	chr5:112075600-112095800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr5:112076000-112090800	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr5:112076000-112095400	Weak transcription	NH-A	brain
39	chr5:112076200-112097000	Weak transcription	NHLF	lung
40	chr5:112078000-112095800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:112078400-112091200	Weak transcription	Primary T cells from cord blood	blood
42	chr5:112078600-112093000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr5:112078600-112095800	Weak transcription	GM12878-XiMat	blood
44	chr5:112078800-112080000	Enhancers	Brain Anterior Caudate	brain
45	chr5:112078800-112083200	Weak transcription	Brain Germinal Matrix	brain
46	chr5:112078800-112092000	Weak transcription	Fetal Brain Male	brain
47	chr5:112078800-112097200	Weak transcription	NHDF-Ad	bronchial
48	chr5:112079000-112080000	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr5:112079000-112080200	Enhancers	Brain Substantia Nigra	brain
50	chr5:112079000-112080400	Enhancers	Brain Cingulate Gyrus	brain

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