Variant report

Variant	rs73172114
Chromosome Location	chr3:158176191-158176192
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10936131	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10936132	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10936139	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10936143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10936144	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10936145	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11707386	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11708784	0.81[AMR][1000 genomes]
rs11710813	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11712563	0.83[AMR][1000 genomes]
rs11716969	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11717923	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11719124	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11719153	0.84[AMR][1000 genomes]
rs12053861	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12053865	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12053869	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12492884	0.81[AMR][1000 genomes]
rs12493128	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12496934	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12631704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12634807	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12636733	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12637649	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12639261	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12639310	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs16829104	0.81[AMR][1000 genomes]
rs17627933	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17628958	0.81[AMR][1000 genomes]
rs17684859	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1851062	0.80[AMR][1000 genomes]
rs1918000	0.84[AMR][1000 genomes]
rs2139696	0.82[AMR][1000 genomes]
rs34434866	0.83[AMR][1000 genomes]
rs4680425	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4680428	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4680432	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4680435	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680441	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55765541	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55842512	0.81[AMR][1000 genomes]
rs56123505	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58195752	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs58925169	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6441193	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6767494	0.82[ASN][1000 genomes]
rs6772246	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6784968	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6788907	0.80[AMR][1000 genomes]
rs6800853	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6806967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6807468	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs73154304	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73154306	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73154307	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73154309	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73154313	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73154314	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73154329	0.81[AMR][1000 genomes]
rs73166358	0.80[AMR][1000 genomes]
rs73168723	0.83[AMR][1000 genomes]
rs73168799	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs73170303	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73170306	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73170310	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73170326	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73170337	0.83[AMR][1000 genomes]
rs73170339	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73170346	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73170364	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73170373	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs73170375	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73172105	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs73172119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73172134	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7613528	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7640075	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7641036	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7652970	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916910	chr3:157926799-158183372	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1014381	chr3:158070451-158350118	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv967206	chr3:158149860-158176292	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs73172114	RP11-538P18.2	cis	Skin Sun Exposed Lower leg	GTEx
rs73172114	RP11-538P18.2	cis	Artery Tibial	GTEx
rs73172114	RSRC1	cis	Adipose Subcutaneous	GTEx
rs73172114	RP11-538P18.2	cis	Nerve Tibial	GTEx
rs73172114	RP11-538P18.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158156400-158176200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:158169600-158182400	Weak transcription	Primary B cells from cord blood	blood
3	chr3:158171400-158177800	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr3:158173200-158178200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:158175800-158176400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:158176000-158176400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links