Variant report

Variant	rs11900117
Chromosome Location	chr2:67795023-67795024
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10184721	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10190391	0.85[AMR][1000 genomes]
rs10204519	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11904407	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11904581	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13398896	1.00[CEU][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034036	0.86[ASN][1000 genomes]
rs6546321	0.86[ASN][1000 genomes]
rs6708296	0.86[ASN][1000 genomes]
rs6726761	0.86[ASN][1000 genomes]
rs6757264	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760771	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72899995	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7568300	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7570412	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7573396	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579880	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7582772	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7589963	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604451	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[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	nsv534389	chr2:67388428-68225338	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv962033	chr2:67794826-67798059	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11900117	PITPNC1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:67789800-67795800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:67790400-67798600	Weak transcription	Pancreas	Pancrea
3	chr2:67790800-67795600	Enhancers	Osteobl	bone
4	chr2:67792000-67795200	Weak transcription	Fetal Heart	heart
5	chr2:67792600-67795400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:67792800-67795600	Enhancers	A549	lung
7	chr2:67793400-67795400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr2:67793400-67795400	Enhancers	NH-A	brain
9	chr2:67793600-67799400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:67793800-67799600	Weak transcription	Psoas Muscle	Psoas
11	chr2:67793800-67800400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:67793800-67803000	Weak transcription	Fetal Stomach	stomach
13	chr2:67794400-67798200	Weak transcription	Stomach Mucosa	stomach
14	chr2:67794400-67798600	Weak transcription	Left Ventricle	heart
15	chr2:67794400-67798600	Weak transcription	NHLF	lung
16	chr2:67794600-67796200	Enhancers	Hela-S3	cervix
17	chr2:67794600-67799000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:67794600-67799400	Weak transcription	HSMMtube	muscle
19	chr2:67794800-67799400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:67795000-67795600	Enhancers	Fetal Lung	lung

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