Variant report

Variant	rs1429039
Chromosome Location	chr5:15586121-15586122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10037317	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13184823	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1366651	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1366653	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1429037	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1429040	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1429041	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1835130	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1835131	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1835132	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1835133	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1978633	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2402166	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2402167	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4702084	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4702086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6420022	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6554887	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6554888	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6895002	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7733607	0.92[CEU][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7734082	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9312893	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9312894	0.92[CEU][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs969351	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs972182	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs983889	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][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	nsv516929	chr5:15087791-15870300	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1023068	chr5:15095221-15863583	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv869040	chr5:15097602-15866117	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv530222	chr5:15151662-15851485	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15574000-15594200	Weak transcription	Fetal Kidney	kidney
2	chr5:15576200-15588000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:15578200-15590200	Weak transcription	Right Ventricle	heart
4	chr5:15578200-15596200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:15578200-15600200	Weak transcription	Left Ventricle	heart
6	chr5:15581000-15604400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr5:15581600-15603400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr5:15582000-15587200	Weak transcription	Ovary	ovary
9	chr5:15584000-15599200	Weak transcription	HSMMtube	muscle
10	chr5:15584400-15587200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:15584400-15587200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:15584600-15586600	Weak transcription	Fetal Stomach	stomach
13	chr5:15584800-15586600	Weak transcription	Brain Hippocampus Middle	brain
14	chr5:15585000-15586600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:15585000-15594600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr5:15585000-15604000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr5:15585000-15606400	Weak transcription	Adipose Nuclei	Adipose
18	chr5:15585000-15630200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:15585200-15586200	Enhancers	Osteobl	bone
20	chr5:15585200-15587600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:15585200-15588400	Enhancers	NHDF-Ad	bronchial
22	chr5:15585200-15594200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:15585200-15594400	Weak transcription	Fetal Muscle Leg	muscle
24	chr5:15585200-15600000	Weak transcription	HSMM	muscle
25	chr5:15585200-15601000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr5:15585200-15602000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr5:15585200-15605200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr5:15585400-15586200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr5:15585400-15587000	Enhancers	Fetal Heart	heart
30	chr5:15585400-15588200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:15585800-15594600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:15586000-15586200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr5:15586000-15586200	Enhancers	Fetal Lung	lung
34	chr5:15586000-15586400	Enhancers	Aorta	Aorta
35	chr5:15586000-15588200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:15586000-15588200	Enhancers	Brain Substantia Nigra	brain
37	chr5:15586000-15588200	Enhancers	Colon Smooth Muscle	Colon
38	chr5:15586000-15619800	Weak transcription	NHLF	lung

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