Variant report

Variant	rs55961288
Chromosome Location	chr2:187560627-187560628
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr2:187558107-187560631	H1-neurons	neurons:	n/a	chr2:187558532-187558539
2	MXI1	chr2:187557978-187560961	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:187560603..187562603-chr2:187566920..187568665,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227227	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10165992	0.89[EUR][1000 genomes]
rs1072901	0.83[ASN][1000 genomes]
rs10755000	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10931253	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12618322	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12620821	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13028008	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1448427	0.87[ASN][1000 genomes]
rs17406229	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17406346	0.81[ASN][1000 genomes]
rs2012128	0.86[EUR][1000 genomes]
rs2121975	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2121976	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2276562	0.82[ASN][1000 genomes]
rs2460766	0.84[EUR][1000 genomes]
rs2595383	0.86[EUR][1000 genomes]
rs2595386	0.87[EUR][1000 genomes]
rs2595395	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2682863	0.88[EUR][1000 genomes]
rs2682868	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2682873	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3213964	0.86[ASN][1000 genomes]
rs34056045	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34840521	0.87[ASN][1000 genomes]
rs35348196	0.87[ASN][1000 genomes]
rs3816375	0.84[ASN][1000 genomes]
rs4667108	0.84[ASN][1000 genomes]
rs4667112	0.81[ASN][1000 genomes]
rs4667113	0.82[ASN][1000 genomes]
rs56222785	0.83[ASN][1000 genomes]
rs62173041	0.81[ASN][1000 genomes]
rs62196185	0.80[ASN][1000 genomes]
rs6705757	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585442	0.82[ASN][1000 genomes]
rs7585471	0.82[ASN][1000 genomes]
rs930657	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9789704	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 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	chr2:187558000-187563000	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr2:187558200-187560800	Active TSS	Brain Hippocampus Middle	brain
3	chr2:187558200-187561200	Active TSS	Brain Angular Gyrus	brain
4	chr2:187558200-187561200	Active TSS	Brain Anterior Caudate	brain
5	chr2:187558600-187561000	Active TSS	Cortex derived primary cultured neurospheres	brain
6	chr2:187558600-187561200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:187558600-187561200	Active TSS	Brain Germinal Matrix	brain
8	chr2:187558600-187561200	Active TSS	Fetal Brain Female	brain
9	chr2:187558600-187561400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:187558800-187561200	Active TSS	Fetal Brain Male	brain
11	chr2:187559000-187560800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:187559400-187560800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr2:187559600-187561200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:187560200-187561000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:187560400-187560800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:187560400-187561000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr2:187560400-187579400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:187560600-187560800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:187560600-187560800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:187560600-187560800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:187560600-187560800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:187560600-187560800	Enhancers	Colon Smooth Muscle	Colon
23	chr2:187560600-187560800	Enhancers	Osteobl	bone
24	chr2:187560600-187561000	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr2:187560600-187561000	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr2:187560600-187561000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:187560600-187561200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:187560600-187561200	Active TSS	Brain Cingulate Gyrus	brain
29	chr2:187560600-187561200	Weak transcription	Brain Substantia Nigra	brain
30	chr2:187560600-187561200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr2:187560600-187561400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:187560600-187561400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:187560600-187562000	Weak transcription	HUVEC	blood vessel
34	chr2:187560600-187562000	Weak transcription	NH-A	brain
35	chr2:187560600-187562200	Weak transcription	NHDF-Ad	bronchial
36	chr2:187560600-187563800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr2:187560600-187566800	Weak transcription	Fetal Kidney	kidney
38	chr2:187560600-187575400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr2:187560600-187582200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:187560600-187584200	Weak transcription	Fetal Lung	lung

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