Variant report

Variant	rs2059900
Chromosome Location	chr5:15595768-15595769
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10520820	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs11748066	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11956557	0.83[CEU][hapmap]
rs12055284	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs13165753	0.86[CEU][hapmap]
rs13165774	0.83[CEU][hapmap]
rs13176043	0.86[EUR][1000 genomes]
rs13177182	0.91[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13177283	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs13184983	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13190262	0.82[CEU][hapmap]
rs1429030	1.00[CEU][hapmap]
rs1429034	0.90[ASN][1000 genomes]
rs17523444	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs17523486	0.82[CEU][hapmap]
rs17523562	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs17647484	0.95[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs17647490	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2964265	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2964271	0.95[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs2964272	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3097352	0.84[ASN][1000 genomes]
rs3097353	0.87[ASN][1000 genomes]
rs35283404	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35336928	0.86[EUR][1000 genomes]
rs3762978	0.94[ASN][1000 genomes]
rs4129028	0.80[EUR][1000 genomes]
rs4440359	0.89[EUR][1000 genomes]
rs4509017	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs4587075	0.90[CEU][hapmap]
rs58149311	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60776566	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6554889	0.94[ASN][1000 genomes]
rs6554891	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs6860057	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs6864426	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6865410	0.83[CEU][hapmap]
rs6871889	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs6872217	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs6878966	0.95[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7706195	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7736101	0.85[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs891196	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
5	nsv830214	chr5:15589809-15791032	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3507774	chr5:15593461-15822407	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3507776	chr5:15593461-15822407	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15578200-15596200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr5:15578200-15600200	Weak transcription	Left Ventricle	heart
3	chr5:15581000-15604400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:15581600-15603400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr5:15584000-15599200	Weak transcription	HSMMtube	muscle
6	chr5:15585000-15604000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr5:15585000-15606400	Weak transcription	Adipose Nuclei	Adipose
8	chr5:15585000-15630200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:15585200-15600000	Weak transcription	HSMM	muscle
10	chr5:15585200-15601000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr5:15585200-15602000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:15585200-15605200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr5:15586000-15619800	Weak transcription	NHLF	lung
14	chr5:15586400-15598800	Weak transcription	Aorta	Aorta
15	chr5:15587400-15596600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:15587400-15600200	Weak transcription	Lung	lung
17	chr5:15587800-15601000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr5:15587800-15601000	Weak transcription	Brain Anterior Caudate	brain
19	chr5:15588200-15598200	Weak transcription	Colon Smooth Muscle	Colon
20	chr5:15588200-15598800	Weak transcription	Brain Substantia Nigra	brain
21	chr5:15588200-15605400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:15588400-15600400	Weak transcription	Brain Hippocampus Middle	brain
23	chr5:15588400-15612600	Weak transcription	NHDF-Ad	bronchial
24	chr5:15588800-15603600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:15590800-15605000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:15593400-15606000	Weak transcription	HUVEC	blood vessel
27	chr5:15593400-15633400	Weak transcription	Fetal Lung	lung
28	chr5:15593600-15600000	Weak transcription	Fetal Stomach	stomach
29	chr5:15593600-15606200	Weak transcription	Fetal Brain Male	brain
30	chr5:15593600-15606400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:15593800-15601000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:15594400-15596000	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr5:15594400-15597600	Enhancers	Fetal Heart	heart
34	chr5:15594800-15595800	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr5:15594800-15605000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:15595000-15596800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:15595000-15601400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:15595200-15595800	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr5:15595200-15596000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr5:15595200-15596200	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr5:15595200-15597000	Weak transcription	Ovary	ovary
42	chr5:15595200-15600200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:15595200-15607800	Weak transcription	Fetal Kidney	kidney
44	chr5:15595400-15596000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr5:15595400-15600000	Weak transcription	Fetal Muscle Leg	muscle
46	chr5:15595600-15597000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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