Variant report

Variant	rs252804
Chromosome Location	chr5:106764106-106764107
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:106763769..106766443-chr5:107007401..107010371,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs252803	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs252805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs252808	0.94[EUR][1000 genomes]
rs252810	0.87[EUR][1000 genomes]
rs252811	0.94[EUR][1000 genomes]
rs252812	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs252814	0.82[EUR][1000 genomes]
rs252815	0.82[EUR][1000 genomes]
rs252818	0.92[EUR][1000 genomes]
rs252819	0.92[EUR][1000 genomes]
rs252983	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs252984	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2562525	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2731839	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2731840	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs431982	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs467472	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs468998	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]

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:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106751600-106764400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr5:106751800-106765800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr5:106751800-106767800	Weak transcription	Stomach Mucosa	stomach
4	chr5:106753400-106764400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:106754000-106767600	Weak transcription	Fetal Stomach	stomach
6	chr5:106756400-106768200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr5:106756600-106772000	Weak transcription	Esophagus	oesophagus
8	chr5:106758600-106765800	Weak transcription	Aorta	Aorta
9	chr5:106758600-106765800	Weak transcription	Fetal Kidney	kidney
10	chr5:106758600-106767800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:106758600-106767800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:106758600-106767800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:106758600-106767800	Weak transcription	Left Ventricle	heart
14	chr5:106758600-106771200	Weak transcription	Right Ventricle	heart
15	chr5:106758600-106772000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:106758600-106785000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:106759400-106764200	Enhancers	HSMM	muscle
18	chr5:106759600-106767600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr5:106760400-106764600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:106761600-106766200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:106761800-106765800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr5:106761800-106767200	Weak transcription	Adipose Nuclei	Adipose
23	chr5:106761800-106767600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr5:106762000-106764400	Enhancers	HMEC	breast
25	chr5:106762200-106767200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:106762200-106767600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:106762200-106767600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr5:106762200-106767600	Weak transcription	HSMMtube	muscle
29	chr5:106762200-106767600	Weak transcription	NH-A	brain
30	chr5:106762200-106771600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr5:106762200-106772200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr5:106762400-106765600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr5:106762400-106765600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr5:106762400-106765600	Weak transcription	NHDF-Ad	bronchial
35	chr5:106762400-106765600	Weak transcription	NHLF	lung
36	chr5:106762400-106765800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:106762600-106767400	Weak transcription	NHEK	skin
38	chr5:106762600-106767600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr5:106762800-106767400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:106763000-106767400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:106763000-106772000	Weak transcription	Right Atrium	heart
42	chr5:106763200-106765200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:106763200-106765800	Weak transcription	HUVEC	blood vessel
44	chr5:106763200-106767200	Weak transcription	Hela-S3	cervix
45	chr5:106763200-106767600	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr5:106763200-106767800	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr5:106763200-106773600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:106763200-106773600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:106763400-106771800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr5:106763800-106764200	Flanking Active TSS	GM12878-XiMat	blood

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