Variant report

Variant	rs1516447
Chromosome Location	chr2:189877565-189877566
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	chr2:189873350..189876277-chr2:189877452..189879284,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs13306270	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2203602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768660	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4666768	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4667256	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4667257	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4667258	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62181744	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62181745	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6715268	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6757347	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7596514	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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	nsv875610	chr2:189796272-189904674	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv875612	chr2:189841052-189878769	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv584061	chr2:189844000-189878769	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189847600-189879200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:189849400-189877600	Strong transcription	Placenta	Placenta
3	chr2:189851800-189878000	Strong transcription	HSMM	muscle
4	chr2:189854000-189878200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:189866400-189879200	Weak transcription	Gastric	stomach
6	chr2:189866600-189878000	Strong transcription	Osteobl	bone
7	chr2:189867400-189878000	Strong transcription	Muscle Satellite Cultured Cells	--
8	chr2:189867600-189878400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:189869000-189878000	Weak transcription	Fetal Intestine Small	intestine
10	chr2:189869200-189877800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:189869200-189877800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr2:189869200-189878800	Weak transcription	Pancreas	Pancrea
13	chr2:189871200-189877800	Strong transcription	Fetal Muscle Leg	muscle
14	chr2:189871600-189884600	Weak transcription	Fetal Kidney	kidney
15	chr2:189871800-189879200	Weak transcription	Fetal Brain Male	brain
16	chr2:189873000-189877600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:189873200-189878200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:189873200-189878600	Weak transcription	Fetal Stomach	stomach
19	chr2:189873200-189885000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:189874000-189878600	Weak transcription	Aorta	Aorta
21	chr2:189874000-189878800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:189874000-189880800	Weak transcription	Left Ventricle	heart
23	chr2:189874200-189878800	Weak transcription	Ovary	ovary
24	chr2:189874200-189879200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr2:189875400-189879000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:189875600-189878400	Strong transcription	NHDF-Ad	bronchial
27	chr2:189876000-189878800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:189876000-189884400	Weak transcription	HSMMtube	muscle
29	chr2:189876200-189898600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:189876400-189878000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:189876400-189878600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr2:189876400-189883400	Weak transcription	NH-A	brain
33	chr2:189876600-189878800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:189876800-189878400	Weak transcription	NHLF	lung
35	chr2:189876800-189878800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:189876800-189879000	Weak transcription	Fetal Lung	lung
37	chr2:189877200-189879400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:189877200-189879400	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:189877400-189886200	Weak transcription	Adipose Nuclei	Adipose
40	chr2:189877400-189897400	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links