Variant report

Variant	rs12140604
Chromosome Location	chr1:222159150-222159151
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10218478	0.81[EUR][1000 genomes]
rs11118926	0.92[EUR][1000 genomes]
rs12022676	0.91[ASN][1000 genomes]
rs12024555	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12025565	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12029332	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12032653	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12032715	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12033415	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12121134	0.92[EUR][1000 genomes]
rs12124556	0.80[EUR][1000 genomes]
rs12125368	0.90[EUR][1000 genomes]
rs12125383	0.96[EUR][1000 genomes]
rs12129860	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12135286	0.84[EUR][1000 genomes]
rs12137323	0.80[EUR][1000 genomes]
rs12731064	0.92[EUR][1000 genomes]
rs12739936	0.92[EUR][1000 genomes]
rs17011141	0.80[EUR][1000 genomes]
rs17011146	0.80[EUR][1000 genomes]
rs17011182	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011200	0.92[EUR][1000 genomes]
rs17442058	0.93[EUR][1000 genomes]
rs17442323	0.92[EUR][1000 genomes]
rs17495159	0.92[EUR][1000 genomes]
rs2095928	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35212520	0.92[EUR][1000 genomes]
rs35718308	0.84[EUR][1000 genomes]
rs35805428	0.92[EUR][1000 genomes]
rs56170536	0.90[EUR][1000 genomes]
rs66732677	0.90[EUR][1000 genomes]
rs6687758	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691195	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695584	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72740077	0.80[EUR][1000 genomes]
rs7520544	0.80[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12140604	RP11-400N13.2	cis	lung	GTEx
rs12140604	RP11-815M8.1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222146200-222163800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:222153200-222161400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr1:222153200-222163800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:222154200-222160800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:222156600-222166000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:222157400-222159600	Weak transcription	NHDF-Ad	bronchial
7	chr1:222157400-222160400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:222157400-222160400	Weak transcription	HSMM	muscle
9	chr1:222157400-222160600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:222157400-222160600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:222157400-222160800	Weak transcription	Osteobl	bone
12	chr1:222157400-222161200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:222157600-222160400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:222157600-222160400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:222157600-222160600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:222157800-222160600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:222158600-222160200	Weak transcription	NHEK	skin
18	chr1:222158800-222159600	Weak transcription	HMEC	breast
19	chr1:222159000-222161000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links