Variant report

Variant	rs58026116
Chromosome Location	chr2:11851725-11851726
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11837517..11840283-chr2:11849750..11852700,2	MCF-7	breast:
2	chr2:11851055..11853217-chr2:11855001..11857096,3	MCF-7	breast:
3	chr2:11850587..11853159-chr2:11857216..11858736,3	K562	blood:
4	chr2:11850587..11853159-chr2:11857216..11858736,2	K562	blood:
5	chr2:11850515..11852161-chr2:11877592..11880491,2	MCF-7	breast:
6	chr2:11850883..11854568-chr2:11860179..11862646,3	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10929766	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11684640	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11684644	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11687567	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11691889	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11893735	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12469060	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12470427	0.81[AMR][1000 genomes]
rs3923671	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3924929	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4366872	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4371339	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4517949	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4614906	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4640359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4640362	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55864809	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56387825	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59341236	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60118851	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7587266	0.81[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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats 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 miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
4	nsv469449	chr2:11808654-11854012	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv580972	chr2:11808654-11854012	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11844200-11854200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr2:11844600-11856400	Weak transcription	Psoas Muscle	Psoas
3	chr2:11848600-11852200	Weak transcription	Placenta	Placenta
4	chr2:11848800-11854600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:11848800-11855400	Weak transcription	Pancreas	Pancrea
6	chr2:11849000-11854400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:11849400-11852800	Enhancers	Brain Cingulate Gyrus	brain
8	chr2:11849800-11852000	Enhancers	Colon Smooth Muscle	Colon
9	chr2:11849800-11852800	Enhancers	NHLF	lung
10	chr2:11849800-11853200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:11849800-11853200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr2:11849800-11853400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:11850000-11852000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:11850000-11852000	Enhancers	Stomach Smooth Muscle	stomach
15	chr2:11850000-11852600	Enhancers	Brain Substantia Nigra	brain
16	chr2:11850000-11852600	Enhancers	Ovary	ovary
17	chr2:11850200-11851800	Enhancers	Fetal Lung	lung
18	chr2:11850200-11851800	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr2:11850200-11852000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:11850200-11852000	Enhancers	Fetal Stomach	stomach
21	chr2:11850200-11852600	Enhancers	Brain Hippocampus Middle	brain
22	chr2:11850200-11852800	Enhancers	Brain Angular Gyrus	brain
23	chr2:11850400-11851800	Enhancers	Fetal Heart	heart
24	chr2:11850400-11852200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr2:11850400-11853000	Enhancers	Brain Anterior Caudate	brain
26	chr2:11850600-11852000	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr2:11850600-11856400	Weak transcription	Hela-S3	cervix
28	chr2:11850800-11851800	Weak transcription	Aorta	Aorta
29	chr2:11850800-11852600	Active TSS	Esophagus	oesophagus
30	chr2:11850800-11852600	Enhancers	Fetal Muscle Leg	muscle
31	chr2:11850800-11853200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:11850800-11856200	Weak transcription	Right Atrium	heart
33	chr2:11851000-11851800	Enhancers	Fetal Brain Male	brain
34	chr2:11851000-11852600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:11851000-11852600	Enhancers	Adipose Nuclei	Adipose
36	chr2:11851200-11852400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:11851200-11852600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:11851200-11853000	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr2:11851400-11852600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:11851400-11852600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:11851400-11852600	Weak transcription	HMEC	breast
42	chr2:11851400-11852600	Weak transcription	NHEK	skin
43	chr2:11851400-11853000	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr2:11851400-11853200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:11851400-11856600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:11851400-11856600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:11851600-11853000	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr2:11851600-11855600	Weak transcription	Liver	Liver

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