Variant report

Variant	rs153409
Chromosome Location	chr5:16790483-16790484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:16788946..16790699-chr5:16935201..16936930,2	MCF-7	breast:
2	chr5:16784701..16787932-chr5:16789785..16793090,3	MCF-7	breast:
3	chr5:16790349..16791141-chr5:17188352..17189070,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145555	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10037139	0.81[EUR][1000 genomes]
rs185236	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs250349	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs250353	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs250356	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs253359	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs253365	0.85[CEU][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes]
rs253366	0.81[AMR][1000 genomes]
rs253367	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs253370	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28297	0.85[CEU][hapmap];0.91[TSI][hapmap]
rs33401	0.81[CEU][hapmap]
rs40020	0.81[CEU][hapmap]
rs451009	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs496033	0.85[CEU][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6888120	0.81[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3529928	chr5:16748426-16856563	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	esv3529929	chr5:16748426-16856563	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv1030550	chr5:16748966-16872084	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16755200-16795400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:16757600-16796800	Weak transcription	Right Ventricle	heart
3	chr5:16760000-16791400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:16761000-16796600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:16763800-16794600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:16764600-16792800	Weak transcription	Stomach Mucosa	stomach
7	chr5:16764600-16807400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:16770200-16791400	Weak transcription	Fetal Kidney	kidney
9	chr5:16770800-16792400	Weak transcription	Placenta	Placenta
10	chr5:16770800-16793800	Weak transcription	Hela-S3	cervix
11	chr5:16775200-16796800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:16778800-16800000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:16779400-16791400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr5:16779800-16796600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:16779800-16797200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:16780200-16791000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:16780800-16791400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr5:16783000-16797000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr5:16783000-16797400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:16783200-16791400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:16783400-16792600	Weak transcription	Lung	lung
22	chr5:16783400-16796800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:16783400-16810000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:16784400-16796800	Weak transcription	HMEC	breast
25	chr5:16784600-16809200	Weak transcription	Ovary	ovary
26	chr5:16784800-16794600	Weak transcription	Gastric	stomach
27	chr5:16785000-16791400	Weak transcription	Psoas Muscle	Psoas
28	chr5:16785200-16791400	Weak transcription	Fetal Lung	lung
29	chr5:16785200-16792400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr5:16785200-16794600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:16785400-16791400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:16785400-16791400	Weak transcription	HSMMtube	muscle
33	chr5:16785400-16792000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr5:16785400-16792400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:16785400-16794600	Weak transcription	Spleen	Spleen
36	chr5:16785400-16796800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:16785600-16790800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr5:16785600-16791400	Weak transcription	Brain Hippocampus Middle	brain
39	chr5:16785800-16791400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr5:16785800-16791400	Weak transcription	Osteobl	bone
41	chr5:16785800-16791600	Weak transcription	NHDF-Ad	bronchial
42	chr5:16785800-16792200	Weak transcription	Fetal Stomach	stomach
43	chr5:16785800-16804200	Weak transcription	HSMM	muscle
44	chr5:16786400-16791400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr5:16786400-16791400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr5:16787800-16790600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:16788000-16791600	Weak transcription	Brain Germinal Matrix	brain
48	chr5:16788000-16792600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr5:16788200-16790800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:16788400-16790600	Strong transcription	HUVEC	blood vessel

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