Variant report

Variant	rs3188408
Chromosome Location	chr5:16673800-16673801
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	chr5:16670338..16672249-chr5:16672358..16674195,2	MCF-7	breast:
2	chr1:9356327..9359278-chr5:16672338..16674681,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs256934	1.00[AMR][1000 genomes]
rs256936	1.00[AMR][1000 genomes]
rs27369	1.00[AMR][1000 genomes]
rs56331036	1.00[AMR][1000 genomes]
rs57469405	1.00[AMR][1000 genomes]
rs58091496	1.00[AMR][1000 genomes]
rs58336311	1.00[AMR][1000 genomes]
rs58840252	1.00[AMR][1000 genomes]
rs61252560	1.00[AMR][1000 genomes]
rs61649363	1.00[AMR][1000 genomes]
rs73051043	1.00[AMR][1000 genomes]
rs73051047	1.00[AMR][1000 genomes]
rs73051049	1.00[AMR][1000 genomes]
rs747057	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869660	chr5:16651289-16766428	Genic enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv522062	chr5:16670618-16679966	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	n/a
3	nsv516145	chr5:16673685-16679966	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16661600-16689400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:16661800-16700000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:16663000-16674800	Weak transcription	Aorta	Aorta
4	chr5:16663000-16712400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:16663400-16676600	Strong transcription	A549	lung
6	chr5:16663600-16695400	Strong transcription	Fetal Intestine Small	intestine
7	chr5:16663800-16676600	Strong transcription	Duodenum Mucosa	Duodenum
8	chr5:16663800-16690800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr5:16663800-16694400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:16663800-16698000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:16663800-16702400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:16663800-16713400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:16664000-16676800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:16664000-16701000	Strong transcription	Fetal Intestine Large	intestine
15	chr5:16664000-16702000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr5:16664000-16702200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:16664000-16702400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:16664200-16702200	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:16664600-16690600	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr5:16664800-16674600	Weak transcription	Small Intestine	intestine
21	chr5:16664800-16677600	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr5:16665600-16676800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:16665600-16699200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:16666200-16676800	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr5:16666200-16680600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:16667200-16674800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr5:16667400-16683600	Weak transcription	Liver	Liver
28	chr5:16667600-16673800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:16667600-16676600	Strong transcription	HSMMtube	muscle
30	chr5:16667800-16674800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr5:16667800-16674800	Weak transcription	Stomach Mucosa	stomach
32	chr5:16667800-16675000	Weak transcription	Left Ventricle	heart
33	chr5:16667800-16676400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr5:16667800-16677400	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr5:16667800-16680000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr5:16667800-16701000	Weak transcription	Right Ventricle	heart
37	chr5:16668000-16676000	Strong transcription	Brain Hippocampus Middle	brain
38	chr5:16668200-16676400	Strong transcription	Placenta	Placenta
39	chr5:16669800-16676200	Strong transcription	HSMM	muscle
40	chr5:16670000-16674200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr5:16670200-16673800	Strong transcription	Brain Substantia Nigra	brain
42	chr5:16670200-16674000	Strong transcription	HMEC	breast
43	chr5:16670200-16676400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr5:16670200-16676800	Strong transcription	Fetal Muscle Leg	muscle
45	chr5:16670200-16678000	Weak transcription	Fetal Heart	heart
46	chr5:16670400-16676000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:16670400-16676200	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr5:16670400-16676400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr5:16670400-16677200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
50	chr5:16670600-16673800	Strong transcription	Colonic Mucosa	Colon

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