Variant report

Variant	rs25997
Chromosome Location	chr5:106819406-106819407
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs25966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs25969	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs25972	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs25976	0.91[MEX][hapmap]
rs25979	0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs25980	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs25981	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs25982	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs25996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26236	0.84[EUR][1000 genomes]
rs26240	0.84[EUR][1000 genomes]
rs27853	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28001	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs31717	0.96[CEU][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs32013	0.85[EUR][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:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106805600-106822600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:106806000-106825600	Weak transcription	Aorta	Aorta
3	chr5:106806200-106822200	Weak transcription	HSMM	muscle
4	chr5:106808400-106837800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:106808600-106822600	Weak transcription	Gastric	stomach
6	chr5:106808800-106822800	Weak transcription	Left Ventricle	heart
7	chr5:106809000-106822800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:106813200-106821400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr5:106814000-106821600	Weak transcription	Right Ventricle	heart
10	chr5:106814400-106821000	Weak transcription	HMEC	breast
11	chr5:106815000-106821600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:106815000-106823000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:106815200-106822800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:106815400-106820800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:106815400-106821400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:106815600-106819800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr5:106815600-106822600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr5:106815800-106821000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:106816200-106822800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr5:106817200-106819800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:106817200-106822400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr5:106817400-106821800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr5:106817600-106820400	Enhancers	Fetal Heart	heart
24	chr5:106817600-106825000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr5:106817600-106829800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr5:106818200-106821600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr5:106818400-106821600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:106818400-106821800	Weak transcription	Stomach Mucosa	stomach
29	chr5:106818400-106825000	Weak transcription	Right Atrium	heart
30	chr5:106818600-106822000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr5:106818800-106821600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:106818800-106821800	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr5:106819000-106820400	Enhancers	A549	lung
34	chr5:106819000-106821000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:106819000-106821600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr5:106819000-106821800	Enhancers	GM12878-XiMat	blood
37	chr5:106819200-106819600	Enhancers	Fetal Lung	lung
38	chr5:106819200-106819600	Weak transcription	NHDF-Ad	bronchial
39	chr5:106819200-106820200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:106819200-106820800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr5:106819200-106821000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:106819400-106819800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:106819400-106819800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr5:106819400-106819800	Enhancers	Fetal Kidney	kidney
45	chr5:106819400-106819800	Weak transcription	Fetal Muscle Leg	muscle
46	chr5:106819400-106820000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr5:106819400-106821600	Enhancers	Cortex derived primary cultured neurospheres	brain

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