Variant report

Variant	rs3955380
Chromosome Location	chr4:120334410-120334411
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10008386	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10008392	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10014719	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10016944	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10017543	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10023569	0.84[AMR][1000 genomes]
rs10024844	0.80[EUR][1000 genomes]
rs10025054	0.80[EUR][1000 genomes]
rs10028669	0.80[AMR][1000 genomes]
rs10518331	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11098513	0.81[EUR][1000 genomes]
rs12504149	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12506148	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12508173	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12512118	0.80[EUR][1000 genomes]
rs13133522	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13151285	0.80[EUR][1000 genomes]
rs2389802	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28572238	0.81[EUR][1000 genomes]
rs28714195	0.81[EUR][1000 genomes]
rs34913743	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35091806	0.83[AMR][1000 genomes]
rs35165976	0.83[AMR][1000 genomes]
rs3890049	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4001207	0.81[AMR][1000 genomes]
rs4079144	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4345162	0.81[EUR][1000 genomes]
rs4604043	0.80[EUR][1000 genomes]
rs59394118	0.80[AMR][1000 genomes]
rs6845714	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6846442	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6846620	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71610279	0.84[AMR][1000 genomes]
rs71610280	0.84[AMR][1000 genomes]
rs71612596	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71612598	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71612602	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7654700	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7654762	0.83[AMR][1000 genomes]
rs7695996	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7696465	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7696649	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7696857	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7696875	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9995234	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9995244	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv879841	chr4:120244085-120388406	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv879842	chr4:120244085-120424087	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv2538163	chr4:120252854-120388678	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv966315	chr4:120323446-120375667	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv879843	chr4:120326323-120502461	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv964147	chr4:120326556-120352949	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3955380	RP11-384K6.6	cis	Whole Blood	GTEx
rs3955380	RP11-33B1.4	cis	Whole Blood	GTEx
rs3955380	RP11-33B1.1	cis	Nerve Tibial	GTEx
rs3955380	RP11-33B1.1	cis	Whole Blood	GTEx
rs3955380	RP11-33B1.1	cis	Esophagus Mucosa	GTEx
rs3955380	RP11-33B1.1	cis	Thyroid	GTEx
rs3955380	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs3955380	RP11-33B1.1	cis	lung	GTEx
rs3955380	RP11-33B1.1	cis	Heart Left Ventricle	GTEx
rs3955380	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120324200-120342200	Weak transcription	Pancreas	Pancrea
2	chr4:120325000-120341200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:120326600-120360800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:120327200-120335200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:120327200-120339200	Weak transcription	Esophagus	oesophagus
6	chr4:120327200-120361400	Weak transcription	Fetal Intestine Small	intestine
7	chr4:120328800-120375200	Weak transcription	Ovary	ovary
8	chr4:120330200-120367600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr4:120330600-120341400	Weak transcription	Adipose Nuclei	Adipose
10	chr4:120330600-120355400	Weak transcription	Liver	Liver
11	chr4:120330600-120365200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:120330600-120366400	Weak transcription	Fetal Stomach	stomach

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