Variant report

Variant	rs17011253
Chromosome Location	chr1:222214056-222214057
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12117316	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12120736	0.82[AMR][1000 genomes]
rs12122410	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126368	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12129517	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12136244	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12137305	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12137800	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12140406	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1339869	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2153352	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2185327	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2378497	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2378498	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2790762	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2800859	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2800860	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2970199	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3121626	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5013041	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55756813	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56054113	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56236427	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61823896	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61823902	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61823903	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61823905	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs996854	0.88[EUR][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	nsv1014333	chr1:222131785-222245578	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17011253	TP53BP2	cis	parietal	SCAN
rs17011253	GPATCH2	cis	parietal	SCAN
rs17011253	IARS2	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222195000-222216000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:222204200-222216600	Weak transcription	Aorta	Aorta
3	chr1:222207000-222217200	Enhancers	Fetal Heart	heart
4	chr1:222211200-222215200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:222211200-222216600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:222211400-222215200	Weak transcription	Osteobl	bone
7	chr1:222211400-222216800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:222211600-222214400	Enhancers	Left Ventricle	heart
9	chr1:222211800-222215200	Weak transcription	HSMMtube	muscle
10	chr1:222212600-222214600	Enhancers	Fetal Muscle Leg	muscle
11	chr1:222212800-222214600	Enhancers	Right Ventricle	heart
12	chr1:222212800-222215200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:222212800-222216600	Weak transcription	Liver	Liver
14	chr1:222213000-222214200	Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr1:222213400-222214200	Enhancers	Rectal Smooth Muscle	rectum
16	chr1:222213600-222214200	Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr1:222213600-222214400	Enhancers	Stomach Smooth Muscle	stomach
18	chr1:222213600-222214600	Enhancers	Colon Smooth Muscle	Colon
19	chr1:222214000-222215200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:222214000-222216200	Weak transcription	Psoas Muscle	Psoas
21	chr1:222214000-222216600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr1:222214000-222216600	Weak transcription	Right Atrium	heart
23	chr1:222214000-222216800	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links