Variant report

Variant	rs25740
Chromosome Location	chr5:106810412-106810413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:106808580..106812777-chr5:106814056..106818233,4	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs17594614	1.00[CEU][hapmap]
rs25964	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs25965	0.85[ASN][1000 genomes]
rs26239	1.00[CEU][hapmap]
rs26241	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26243	0.83[ASN][1000 genomes]
rs26244	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs26247	0.89[YRI][hapmap]
rs27929	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28024	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28112	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28208	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28764	1.00[CEU][hapmap]
rs2898622	1.00[CEU][hapmap]
rs29543	0.89[YRI][hapmap]
rs41493053	1.00[CEU][hapmap]
rs636137	0.96[YRI][hapmap]

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:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106799600-106811200	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr5:106799600-106811800	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr5:106799800-106811000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:106802600-106813600	Weak transcription	Right Ventricle	heart
5	chr5:106803600-106812600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:106803800-106811400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr5:106805600-106812200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:106805600-106822600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:106806000-106825600	Weak transcription	Aorta	Aorta
10	chr5:106806200-106810600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:106806200-106811600	Enhancers	NHEK	skin
12	chr5:106806200-106813400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:106806200-106813600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:106806200-106822200	Weak transcription	HSMM	muscle
15	chr5:106806400-106813800	Weak transcription	NHDF-Ad	bronchial
16	chr5:106806600-106811600	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr5:106806800-106815600	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr5:106808000-106811200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:106808000-106812600	Enhancers	Stomach Mucosa	stomach
20	chr5:106808200-106810800	Enhancers	H1 Cell Line	embryonic stem cell
21	chr5:106808200-106812200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr5:106808400-106810800	Enhancers	Primary T cells fromperipheralblood	blood
23	chr5:106808400-106813200	Enhancers	Placenta Amnion	Placenta Amnion
24	chr5:106808400-106837800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr5:106808600-106810600	Weak transcription	Fetal Kidney	kidney
26	chr5:106808600-106813800	Weak transcription	Esophagus	oesophagus
27	chr5:106808600-106822600	Weak transcription	Gastric	stomach
28	chr5:106808800-106810600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:106808800-106810600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr5:106808800-106811800	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr5:106808800-106813800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:106808800-106822800	Weak transcription	Left Ventricle	heart
33	chr5:106809000-106811800	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr5:106809000-106822800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr5:106809200-106814800	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr5:106809400-106814000	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr5:106809600-106812400	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr5:106809600-106812600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:106809800-106811000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr5:106809800-106811400	Enhancers	HMEC	breast
41	chr5:106809800-106811600	Enhancers	Fetal Intestine Small	intestine
42	chr5:106809800-106812400	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr5:106809800-106812800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:106809800-106814600	Enhancers	HUVEC	blood vessel
45	chr5:106810000-106811200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:106810000-106811400	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr5:106810000-106811600	Flanking Active TSS	A549	lung
48	chr5:106810000-106814200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr5:106810000-106814400	Enhancers	Fetal Heart	heart
50	chr5:106810200-106810600	Enhancers	Primary monocytes fromperipheralblood	blood

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