Variant report

Variant	rs12979090
Chromosome Location	chr19:51568066-51568067
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	chr19:51529957..51532626-chr19:51566053..51568758,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167757	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10500306	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11665682	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2736431	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2736433	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2736434	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv524556	chr19:51565975-51572068	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv34104	chr19:51566170-51641675	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv819004	chr19:51566937-51569403	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51565800-51568800	Enhancers	Pancreas	Pancrea
2	chr19:51567200-51568600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:51567800-51568200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:51567800-51568200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr19:51567800-51568200	Flanking Active TSS	K562	blood
6	chr19:51567800-51568400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr19:51567800-51568400	Active TSS	Right Atrium	heart
8	chr19:51567800-51568400	Bivalent/Poised TSS	NHEK	skin
9	chr19:51567800-51568600	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr19:51567800-51568600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
11	chr19:51567800-51568800	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr19:51567800-51568800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:51567800-51568800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:51567800-51568800	Active TSS	A549	lung
15	chr19:51567800-51569000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr19:51567800-51569000	Active TSS	H9 Cell Line	embryonic stem cell
17	chr19:51567800-51569000	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr19:51567800-51569000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr19:51567800-51569000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:51567800-51569000	Enhancers	Gastric	stomach
21	chr19:51567800-51569200	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr19:51567800-51569200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr19:51567800-51569200	Enhancers	Right Ventricle	heart
24	chr19:51568000-51568200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
25	chr19:51568000-51568200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
26	chr19:51568000-51568200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
27	chr19:51568000-51568200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:51568000-51568200	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:51568000-51568200	Bivalent Enhancer	Adipose Nuclei	Adipose
30	chr19:51568000-51568200	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
31	chr19:51568000-51568200	Bivalent Enhancer	Fetal Brain Male	brain
32	chr19:51568000-51568200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
33	chr19:51568000-51568200	Flanking Active TSS	Ovary	ovary
34	chr19:51568000-51568200	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
35	chr19:51568000-51568200	Bivalent Enhancer	Spleen	Spleen
36	chr19:51568000-51568200	Flanking Active TSS	HMEC	breast
37	chr19:51568000-51568200	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
38	chr19:51568000-51568400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:51568000-51568400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
40	chr19:51568000-51568400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
41	chr19:51568000-51568400	Active TSS	Left Ventricle	heart
42	chr19:51568000-51568400	Bivalent/Poised TSS	Thymus	Thymus
43	chr19:51568000-51568600	Active TSS	H1 Cell Line	embryonic stem cell
44	chr19:51568000-51568600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr19:51568000-51568600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
46	chr19:51568000-51568600	Active TSS	Esophagus	oesophagus
47	chr19:51568000-51568600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
48	chr19:51568000-51568600	Bivalent Enhancer	Placenta	Placenta
49	chr19:51568000-51568600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
50	chr19:51568000-51568800	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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