Variant report

Variant	rs12140722
Chromosome Location	chr1:213091573-213091574
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:213081058..213082812-chr1:213090244..213092808,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10864028	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10864029	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11120067	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11576311	0.85[EUR][1000 genomes]
rs11582817	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11586314	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11586464	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12140754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12184323	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1284863	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3816952	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3816953	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3816956	0.99[ASN][1000 genomes]
rs3816957	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951474	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4951655	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6656128	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6656232	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6666277	0.81[AMR][1000 genomes]
rs6670064	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6679848	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6679938	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6679951	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7523310	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7523329	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7533476	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7533575	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs870547	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs871767	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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	nsv1008383	chr1:213025546-213114894	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs12140722	FLVCR1-AS1	cis	Nerve Tibial	GTEx
rs12140722	FLVCR1-AS1	cis	Heart Left Ventricle	GTEx
rs12140722	LQK1	cis	lesional skin	skin_eQTL
rs12140722	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs12140722	FLVCR1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs12140722	FLVCR1-AS1	cis	lung	GTEx
rs12140722	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs12140722	LQK1	cis	uninvolved skin	skin_eQTL
rs12140722	VASH2	Cis_1M	lymphoblastoid	RTeQTL
rs12140722	FLVCR1-AS1	cis	Thyroid	GTEx
rs12140722	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs12140722	LQK1	cis	normal skin	skin_eQTL
rs12140722	FLVCR1-AS1	cis	Whole Blood	GTEx
rs12140722	FLVCR1-AS1	cis	Artery Tibial	GTEx
rs12140722	FLVCR1	cis	multi-tissue	Pritchard
rs12140722	FLVCR1-AS1	cis	Artery Aorta	GTEx
rs12140722	FLVCR1-AS1	cis	Esophagus Mucosa	GTEx
rs12140722	FLVCR1-AS1	cis	Stomach	GTEx
rs12140722	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213086800-213094400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:213089400-213091600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:213090600-213092800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:213090600-213093200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:213090600-213101800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:213090800-213092000	Weak transcription	GM12878-XiMat	blood
7	chr1:213090800-213092600	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:213090800-213101200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:213090800-213101200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:213090800-213101200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:213091200-213091600	Enhancers	H9 Cell Line	embryonic stem cell
12	chr1:213091200-213092200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:213091200-213095000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:213091400-213091800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr1:213091400-213092600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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