Variant report

Variant	rs2400440
Chromosome Location	chr5:147298497-147298498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10077849	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10463392	0.81[EUR][1000 genomes]
rs10477357	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168004	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1368409	0.80[EUR][1000 genomes]
rs1368411	0.80[EUR][1000 genomes]
rs1432977	0.89[AMR][1000 genomes]
rs1432978	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1862330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864994	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2098649	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400441	0.98[GIH][hapmap]
rs34336493	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4502808	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60172148	0.80[EUR][1000 genomes]
rs6580510	0.80[EUR][1000 genomes]
rs6867813	0.80[EUR][1000 genomes]
rs6877693	0.85[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6887251	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7721995	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7736073	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021356	chr5:147103627-147310531	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1033907	chr5:147109014-147309076	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv537916	chr5:147109014-147309076	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3334831	chr5:147165950-147339765	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1028477	chr5:147255013-147416217	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv525042	chr5:147298497-147302214	Enhancers Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
7	nsv528013	chr5:147298497-147302941	Enhancers Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2400440	EEF1GP2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147292400-147300400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:147297200-147298600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr5:147297400-147299000	Enhancers	NHEK	skin
4	chr5:147297600-147298800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:147297600-147299400	Enhancers	Hela-S3	cervix
6	chr5:147297800-147299400	Enhancers	NH-A	brain
7	chr5:147298000-147298800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:147298000-147298800	Enhancers	HMEC	breast
9	chr5:147298000-147299600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:147298000-147300200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:147298200-147300200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:147298400-147299800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr5:147298400-147300400	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links