Variant report

Variant	rs2562554
Chromosome Location	chr5:36571519-36571520
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10061650	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10076624	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10805623	0.92[ASN][1000 genomes]
rs1366636	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2115521	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2562559	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2562568	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2731901	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2731906	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731907	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2731909	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2731920	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9800255	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492319	chr5:36570707-37061019	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2562554	C9	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36569200-36571600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr5:36569200-36571800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr5:36569600-36571600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:36569800-36571600	Enhancers	Fetal Brain Male	brain
5	chr5:36569800-36571600	Enhancers	Left Ventricle	heart
6	chr5:36569800-36573200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:36570000-36572000	Weak transcription	Ovary	ovary
8	chr5:36570000-36572800	Weak transcription	HMEC	breast
9	chr5:36570000-36573200	Weak transcription	NHEK	skin
10	chr5:36570000-36575600	Weak transcription	Aorta	Aorta
11	chr5:36570200-36574000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:36570600-36571600	Enhancers	Brain Angular Gyrus	brain
13	chr5:36570800-36573200	Weak transcription	NHDF-Ad	bronchial
14	chr5:36570800-36573400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr5:36571000-36572200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr5:36571000-36573000	Weak transcription	NH-A	brain
17	chr5:36571000-36575200	Weak transcription	Fetal Heart	heart
18	chr5:36571200-36573200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:36571200-36573200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:36571200-36573400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:36571200-36584000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr5:36571200-36584000	Weak transcription	Brain Substantia Nigra	brain
23	chr5:36571400-36571600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:36571400-36572600	Weak transcription	Osteobl	bone
25	chr5:36571400-36572800	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links