Variant report

Variant	rs29543
Chromosome Location	chr5:106806438-106806439
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	chr5:106802607..106804706-chr5:106804946..106806862,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs25740	0.89[YRI][hapmap]
rs26241	0.92[LWK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs26247	0.88[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs27929	0.90[AFR][1000 genomes]
rs28112	0.82[AFR][1000 genomes]
rs28208	0.87[AFR][1000 genomes]
rs636137	0.88[ASW][hapmap];0.93[YRI][hapmap]

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	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
5	nsv462379	chr5:106789764-106806438	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv471037	chr5:106789764-106806438	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv599334	chr5:106789764-106806438	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106799600-106806800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:106799600-106807000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:106799600-106807200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:106799600-106808200	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr5:106799600-106811200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr5:106799600-106811800	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr5:106799800-106811000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:106802400-106807000	Enhancers	Hela-S3	cervix
9	chr5:106802400-106810200	Weak transcription	Right Atrium	heart
10	chr5:106802600-106808200	Weak transcription	Gastric	stomach
11	chr5:106802600-106813600	Weak transcription	Right Ventricle	heart
12	chr5:106803600-106808200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:106803600-106808400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:106803600-106812600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:106803800-106807000	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr5:106803800-106811400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr5:106804200-106809800	Weak transcription	Fetal Intestine Small	intestine
18	chr5:106804400-106810200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr5:106804600-106810200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr5:106804800-106806600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:106804800-106810400	Weak transcription	Fetal Lung	lung
22	chr5:106805000-106808400	Weak transcription	Left Ventricle	heart
23	chr5:106805000-106809800	Weak transcription	Lung	lung
24	chr5:106805400-106808400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr5:106805400-106809600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:106805400-106810200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr5:106805600-106810400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr5:106805600-106812200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr5:106805600-106822600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:106805800-106807800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr5:106805800-106808400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr5:106805800-106809800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr5:106805800-106810200	Weak transcription	GM12878-XiMat	blood
34	chr5:106806000-106807000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr5:106806000-106807000	Enhancers	HUVEC	blood vessel
36	chr5:106806000-106808200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr5:106806000-106808200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:106806000-106808200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:106806000-106808200	Weak transcription	Esophagus	oesophagus
40	chr5:106806000-106808200	Weak transcription	Fetal Kidney	kidney
41	chr5:106806000-106808200	Weak transcription	Placenta	Placenta
42	chr5:106806000-106809800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr5:106806000-106810200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:106806000-106810200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:106806000-106810200	Weak transcription	Small Intestine	intestine
46	chr5:106806000-106810400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr5:106806000-106825600	Weak transcription	Aorta	Aorta
48	chr5:106806200-106806600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr5:106806200-106807400	Enhancers	HMEC	breast
50	chr5:106806200-106808200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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