Variant report

Variant	rs12992403
Chromosome Location	chr2:67853282-67853283
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:67852630..67855318-chr2:67906179..67908434,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10490723	0.88[ASN][1000 genomes]
rs12477088	0.94[ASN][1000 genomes]
rs12618268	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12986714	0.83[ASN][1000 genomes]
rs12987509	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12989021	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12993096	0.83[ASN][1000 genomes]
rs12997331	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13003698	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13005138	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13013880	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13019532	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13021903	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13023342	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13025342	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13025376	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13028371	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1430786	0.87[ASN][1000 genomes]
rs17033996	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2861683	0.91[ASN][1000 genomes]
rs2861685	0.90[ASN][1000 genomes]
rs2861691	0.92[ASN][1000 genomes]
rs34724856	0.89[ASN][1000 genomes]
rs35002785	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35179846	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35820615	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4362542	0.92[ASN][1000 genomes]
rs4465757	0.84[ASN][1000 genomes]
rs4542832	0.88[ASN][1000 genomes]
rs4671187	0.80[CHB][hapmap]
rs62156279	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6546315	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6546319	0.91[ASN][1000 genomes]
rs6731513	0.88[ASN][1000 genomes]
rs6732490	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6746168	0.89[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs6756226	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6760893	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9789546	0.84[ASN][1000 genomes]
rs980226	0.87[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12992403	SNRPG	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:67852200-67854400	Enhancers	Muscle Satellite Cultured Cells	--
2	chr2:67852400-67853800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr2:67852400-67854200	Enhancers	HMEC	breast
4	chr2:67852400-67854600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:67852400-67854600	Enhancers	NHDF-Ad	bronchial
6	chr2:67852400-67855000	Enhancers	HSMM	muscle
7	chr2:67852600-67853600	Enhancers	Osteobl	bone
8	chr2:67852600-67853800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:67852800-67853400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:67853000-67853400	Enhancers	Fetal Stomach	stomach
11	chr2:67853000-67853400	Flanking Active TSS	HSMMtube	muscle
12	chr2:67853000-67853800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:67853000-67853800	Enhancers	Fetal Muscle Leg	muscle
14	chr2:67853000-67854600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:67853200-67853400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:67853200-67853400	Enhancers	NH-A	brain
17	chr2:67853200-67853600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:67853200-67854000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:67853200-67854600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links