Variant report

Variant	rs13018066
Chromosome Location	chr2:179099946-179099947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179099293..179101307-chr2:179105250..179107076,2	K562	blood:
2	chr2:179090398..179094445-chr2:179099557..179102504,4	K562	blood:
3	chr2:179095589..179097417-chr2:179099252..179101022,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10445766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10445767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12995008	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12999507	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13003146	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13026005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17592042	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs34479159	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62177227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1011423	chr2:179084407-179166160	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13018066	SP9	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179079000-179101200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr2:179091000-179106400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:179091200-179101200	Weak transcription	Psoas Muscle	Psoas
4	chr2:179091200-179115000	Weak transcription	Aorta	Aorta
5	chr2:179092200-179102400	Weak transcription	NHDF-Ad	bronchial
6	chr2:179097800-179100200	Enhancers	NHEK	skin
7	chr2:179098000-179101200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:179098000-179101200	Enhancers	HMEC	breast
9	chr2:179098200-179102400	Weak transcription	NH-A	brain
10	chr2:179098400-179100000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:179098400-179103000	Weak transcription	A549	lung
12	chr2:179098600-179102400	Weak transcription	Osteobl	bone
13	chr2:179098600-179106600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:179099000-179101200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:179099400-179104200	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr2:179099600-179100000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:179099800-179101000	Weak transcription	Hela-S3	cervix
18	chr2:179099800-179102200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:179099800-179102600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:179099800-179102800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links