Variant report

Variant	rs12123727
Chromosome Location	chr1:171665508-171665509
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171665381..171668263-chr1:171669803..171671698,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1001373	0.83[EUR][1000 genomes]
rs10489249	0.82[EUR][1000 genomes]
rs10489251	0.83[EUR][1000 genomes]
rs1052676	0.85[EUR][1000 genomes]
rs10903	0.84[EUR][1000 genomes]
rs10913489	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10913490	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10913492	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10913511	0.84[EUR][1000 genomes]
rs10913514	0.84[EUR][1000 genomes]
rs10913529	0.83[EUR][1000 genomes]
rs10913565	0.81[EUR][1000 genomes]
rs10913582	0.83[EUR][1000 genomes]
rs10913587	0.83[EUR][1000 genomes]
rs11576221	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11577073	0.83[EUR][1000 genomes]
rs11577197	0.83[EUR][1000 genomes]
rs11577745	0.83[EUR][1000 genomes]
rs11578179	0.84[EUR][1000 genomes]
rs11578699	0.83[EUR][1000 genomes]
rs11578723	0.83[EUR][1000 genomes]
rs11579698	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11580415	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11580522	0.83[EUR][1000 genomes]
rs11583920	0.83[EUR][1000 genomes]
rs11590680	0.83[EUR][1000 genomes]
rs11590714	0.83[EUR][1000 genomes]
rs11799420	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11801846	0.83[EUR][1000 genomes]
rs11803174	0.83[EUR][1000 genomes]
rs11808099	0.83[EUR][1000 genomes]
rs11811780	0.81[EUR][1000 genomes]
rs12118409	0.85[AFR][1000 genomes]
rs12119232	0.81[EUR][1000 genomes]
rs12119553	0.81[AMR][1000 genomes]
rs12127026	0.85[EUR][1000 genomes]
rs12128536	0.84[EUR][1000 genomes]
rs12132221	0.83[EUR][1000 genomes]
rs15655	0.84[EUR][1000 genomes]
rs17649050	0.83[EUR][1000 genomes]
rs17649068	0.82[EUR][1000 genomes]
rs2298914	0.81[EUR][1000 genomes]
rs3766653	0.83[EUR][1000 genomes]
rs55670848	0.83[EUR][1000 genomes]
rs56220250	0.83[AMR][1000 genomes]
rs58455759	0.83[EUR][1000 genomes]
rs6656003	0.83[EUR][1000 genomes]
rs6659874	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6667559	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6669263	0.83[EUR][1000 genomes]
rs6678890	0.83[EUR][1000 genomes]
rs6679354	0.85[EUR][1000 genomes]
rs7528057	0.84[AMR][1000 genomes]
rs7536436	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7536543	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9661596	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9662174	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9662853	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12123727	VAMP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171657800-171665800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:171664000-171668400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:171664200-171667600	Weak transcription	Left Ventricle	heart
4	chr1:171664400-171685800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:171664600-171674400	Weak transcription	Primary T cells from cord blood	blood
6	chr1:171664800-171668200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:171664800-171684800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr1:171665000-171669000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:171665000-171692000	Weak transcription	Brain Substantia Nigra	brain
10	chr1:171665400-171665800	Weak transcription	Aorta	Aorta
11	chr1:171665400-171674600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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