Variant report

Variant	rs252808
Chromosome Location	chr5:106736946-106736947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs252803	0.94[CEU][hapmap];0.81[CHB][hapmap];0.96[EUR][1000 genomes]
rs252804	0.94[EUR][1000 genomes]
rs252805	0.94[CEU][hapmap];0.81[CHB][hapmap];0.95[EUR][1000 genomes]
rs252810	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs252811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs252812	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs252814	0.88[EUR][1000 genomes]
rs252815	0.88[EUR][1000 genomes]
rs252818	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs252819	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs252983	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs252984	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2562525	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2731839	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2731840	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs431982	1.00[CEU][hapmap];0.92[CHB][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs467472	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs468998	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[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	nsv1030118	chr5:106006097-106847949	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106720400-106740800	Weak transcription	Aorta	Aorta
2	chr5:106725800-106740400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:106728400-106738200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:106730400-106737200	Weak transcription	Fetal Lung	lung
5	chr5:106731600-106738200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:106732200-106737800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr5:106732200-106738200	Weak transcription	HSMM	muscle
8	chr5:106732200-106739400	Weak transcription	GM12878-XiMat	blood
9	chr5:106732200-106753200	Weak transcription	Fetal Kidney	kidney
10	chr5:106732400-106737400	Weak transcription	Fetal Heart	heart
11	chr5:106732400-106737600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:106732400-106737800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:106732800-106737200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:106733000-106738200	Weak transcription	Ovary	ovary
15	chr5:106733000-106738400	Weak transcription	Left Ventricle	heart
16	chr5:106733600-106744800	Weak transcription	Right Ventricle	heart
17	chr5:106734200-106737200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:106734200-106737800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr5:106734400-106738200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:106735200-106741200	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr5:106735200-106741400	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr5:106735800-106737600	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr5:106736000-106740000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:106736000-106740000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:106736200-106737600	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr5:106736200-106742200	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr5:106736400-106738000	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr5:106736400-106740200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:106736400-106741200	Enhancers	A549	lung
30	chr5:106736600-106738000	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr5:106736600-106740600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr5:106736800-106738800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:106736800-106740000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:106736800-106740200	Enhancers	HUES6 Cell Line	embryonic stem cell

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