Variant report

Variant	rs59752876
Chromosome Location	chr2:98567043-98567044
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	chr2:98541538..98543544-chr2:98565901..98567946,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs55853292	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55887737	0.86[AMR][1000 genomes]
rs58690282	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59049638	0.86[EUR][1000 genomes]
rs59444417	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59635122	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61363543	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62154549	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62154552	0.80[EUR][1000 genomes]
rs62154553	0.80[EUR][1000 genomes]
rs62154555	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62154556	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62154558	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62156480	0.86[EUR][1000 genomes]
rs62156482	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62156488	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156507	0.90[EUR][1000 genomes]
rs62156508	0.93[EUR][1000 genomes]
rs62156509	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62156514	0.90[EUR][1000 genomes]
rs62156519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62156522	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156523	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156524	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156525	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156526	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62156527	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62156530	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62158265	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62158266	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62158268	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62158269	0.86[EUR][1000 genomes]
rs62158270	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62158272	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73960433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73960434	0.89[AFR][1000 genomes]
rs73960435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7575922	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7600204	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7606272	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv960975	chr2:98562321-98567447	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98554000-98570200	Weak transcription	Primary B cells from cord blood	blood
2	chr2:98559800-98567800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:98561800-98570200	Weak transcription	Primary T cells from cord blood	blood
4	chr2:98562000-98567400	Weak transcription	Brain Substantia Nigra	brain
5	chr2:98562200-98570400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:98562400-98569200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:98562600-98567200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr2:98562600-98567600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:98562600-98567800	Weak transcription	Liver	Liver
10	chr2:98562600-98568000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr2:98562600-98570000	Weak transcription	Fetal Intestine Small	intestine
12	chr2:98562600-98570200	Weak transcription	Fetal Lung	lung
13	chr2:98562800-98567800	Weak transcription	Right Atrium	heart
14	chr2:98563200-98567200	Weak transcription	Stomach Mucosa	stomach
15	chr2:98563400-98570600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:98563600-98569600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:98563600-98589200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:98564600-98567400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:98564600-98567600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:98564600-98580600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:98565400-98569200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:98565600-98568400	Enhancers	HMEC	breast
23	chr2:98565800-98567200	Enhancers	Small Intestine	intestine
24	chr2:98565800-98567600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr2:98565800-98568400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:98565800-98568400	Enhancers	NHLF	lung
27	chr2:98566000-98567800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr2:98566000-98568200	Enhancers	Left Ventricle	heart
29	chr2:98566000-98569400	Enhancers	Placenta	Placenta
30	chr2:98566200-98567200	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr2:98566200-98567800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:98566200-98568400	Enhancers	HSMM	muscle
33	chr2:98566200-98570600	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr2:98566400-98568000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:98566400-98568200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:98566400-98568200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:98566400-98568200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:98566400-98568200	Weak transcription	Aorta	Aorta
39	chr2:98566400-98568200	Enhancers	Placenta Amnion	Placenta Amnion
40	chr2:98566400-98568200	Enhancers	NH-A	brain
41	chr2:98566400-98568400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:98566400-98568400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:98566400-98568600	Enhancers	NHDF-Ad	bronchial
44	chr2:98566600-98568200	Enhancers	Adipose Nuclei	Adipose
45	chr2:98566600-98571000	Enhancers	Primary B cells from peripheral blood	blood
46	chr2:98566800-98567200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:98566800-98567200	Enhancers	Esophagus	oesophagus
48	chr2:98566800-98567200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr2:98566800-98567200	Flanking Active TSS	Osteobl	bone
50	chr2:98566800-98567400	Enhancers	Ovary	ovary

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