Variant report

Variant	rs12523004
Chromosome Location	chr5:56994198-56994199
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:56991984..56994307-chr5:57002292..57003964,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10057804	0.81[EUR][1000 genomes]
rs10487615	0.81[EUR][1000 genomes]
rs10940574	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12514617	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12514618	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12520466	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12522697	0.81[EUR][1000 genomes]
rs12654040	0.81[EUR][1000 genomes]
rs16887298	0.81[EUR][1000 genomes]
rs17689645	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17689832	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2160057	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2192367	0.81[EUR][1000 genomes]
rs2192368	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2215419	0.81[EUR][1000 genomes]
rs2898027	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58041565	0.81[EUR][1000 genomes]
rs58266257	0.81[EUR][1000 genomes]
rs62358372	0.98[EUR][1000 genomes]
rs62358374	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62358380	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62358381	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62361169	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6862527	0.81[EUR][1000 genomes]
rs6870485	0.81[EUR][1000 genomes]
rs6894116	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72767430	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72767434	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72767441	0.80[EUR][1000 genomes]
rs741181	0.80[EUR][1000 genomes]
rs7714714	0.81[EUR][1000 genomes]
rs7717808	0.81[EUR][1000 genomes]
rs7734079	0.81[EUR][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	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830310	chr5:56989346-57176006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:56987400-56994800	Weak transcription	Right Ventricle	heart
2	chr5:56988600-56995400	Enhancers	Adipose Nuclei	Adipose
3	chr5:56989400-56996000	Enhancers	Fetal Heart	heart
4	chr5:56989600-56994600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:56989600-56996400	Weak transcription	Psoas Muscle	Psoas
6	chr5:56990000-56995200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:56990200-57005600	Weak transcription	NH-A	brain
8	chr5:56990400-56996200	Enhancers	HMEC	breast
9	chr5:56990600-56995000	Enhancers	Ovary	ovary
10	chr5:56990600-56996600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr5:56991400-56995000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:56991400-56996000	Enhancers	NHEK	skin
13	chr5:56991600-56994600	Weak transcription	Aorta	Aorta
14	chr5:56992000-56995600	Enhancers	HUVEC	blood vessel
15	chr5:56992200-56994800	Weak transcription	Right Atrium	heart
16	chr5:56992200-56996800	Enhancers	Fetal Lung	lung
17	chr5:56992400-56995000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr5:56992400-56995400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:56992400-56995400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:56992400-57004400	Weak transcription	Left Ventricle	heart
21	chr5:56992800-56994200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:56992800-56995000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr5:56993000-56994200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:56993000-56994200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:56993000-56994400	Weak transcription	NHLF	lung
26	chr5:56993000-56994800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:56993000-56994800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:56993200-56994600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:56993400-56994600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr5:56993600-56994200	Enhancers	Colon Smooth Muscle	Colon
31	chr5:56993600-56994800	Enhancers	HSMM	muscle
32	chr5:56993600-56995200	Enhancers	A549	lung
33	chr5:56993600-56995400	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr5:56993800-56994200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr5:56993800-56994600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr5:56993800-56994800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr5:56994000-56994200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:56994000-56994200	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr5:56994000-56994200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:56994000-56994400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr5:56994000-56994800	Enhancers	Muscle Satellite Cultured Cells	--

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