Variant report

Variant	rs12596851
Chromosome Location	chr16:70655967-70655968
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11865702	0.84[ASN][1000 genomes]
rs12051132	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12596022	0.85[ASN][1000 genomes]
rs12596821	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12596861	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12596931	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12599245	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12708905	0.89[ASN][1000 genomes]
rs12917749	0.86[ASN][1000 genomes]
rs12923782	0.84[AFR][1000 genomes]
rs12924106	0.89[ASN][1000 genomes]
rs12928124	0.83[ASN][1000 genomes]
rs12932251	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs13330163	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34538878	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34878593	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3813904	0.83[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4985412	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985539	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4985540	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985541	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4985543	0.84[AFR][1000 genomes]
rs4985544	0.82[ASN][1000 genomes]
rs4985548	0.89[ASN][1000 genomes]
rs4985555	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs6499328	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6499329	0.86[ASN][1000 genomes]
rs6499330	0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7193968	0.86[ASN][1000 genomes]
rs72792838	0.85[ASN][1000 genomes]
rs8053536	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8061569	0.84[ASN][1000 genomes]
rs8061854	0.80[EUR][1000 genomes];0.88[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	esv14380	chr16:70650573-70660117	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12596851	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs12596851	CLEC18A	cis	Whole Blood	GTEx
rs12596851	IL34	cis	lung	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70647400-70669200	Weak transcription	Right Atrium	heart
2	chr16:70647800-70664800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr16:70652400-70656800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr16:70652800-70656000	Active TSS	H1 Cell Line	embryonic stem cell
5	chr16:70652800-70656000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr16:70653200-70656000	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr16:70653400-70656000	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr16:70653800-70656000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr16:70655200-70656000	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr16:70655200-70657000	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr16:70655400-70656000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr16:70655400-70656200	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr16:70655600-70656800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr16:70655800-70656000	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
15	chr16:70655800-70656000	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr16:70655800-70656000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links