Variant report

Variant	rs2675979
Chromosome Location	chr5:40914430-40914431
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10512751	0.86[CEU][hapmap];0.85[CHD][hapmap];0.82[TSI][hapmap]
rs11744119	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs178929	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1812960	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1827364	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1910015	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2122570	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271709	1.00[ASW][hapmap];0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2455305	0.93[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2675981	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs324056	0.93[CEU][hapmap]
rs324062	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs324064	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs324070	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs324071	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs324073	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3792637	0.93[CEU][hapmap];0.85[CHD][hapmap]
rs4360083	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4957358	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs59027389	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60480205	0.95[ASN][1000 genomes]
rs6888489	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6890698	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.97[ASN][1000 genomes]
rs6895317	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73088503	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73088510	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7702096	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7715597	0.89[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7725655	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881467	chr5:40869802-41008650	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2757114	chr5:40874078-41009282	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759341	chr5:40874078-41009282	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv823055	chr5:40875708-41004839	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv35077	chr5:40875843-41000671	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv830268	chr5:40897361-41138366	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2675979	C5orf34	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40905400-40915000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr5:40905600-40915000	Weak transcription	Gastric	stomach
3	chr5:40908800-40916000	Active TSS	Stomach Smooth Muscle	stomach
4	chr5:40909200-40916800	Active TSS	Right Atrium	heart
5	chr5:40909600-40915000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:40909600-40915000	Active TSS	Ovary	ovary
7	chr5:40909800-40915000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:40910000-40915200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:40910200-40915000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:40910600-40915000	Weak transcription	Liver	Liver
11	chr5:40911800-40914600	Weak transcription	Fetal Heart	heart
12	chr5:40911800-40915000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr5:40911800-40915000	Weak transcription	Left Ventricle	heart
14	chr5:40912000-40914800	Weak transcription	Right Ventricle	heart
15	chr5:40912200-40914600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:40913200-40914600	Weak transcription	Fetal Lung	lung
17	chr5:40913800-40914800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr5:40914200-40914600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:40914400-40916000	Active TSS	Duodenum Smooth Muscle	Duodenum

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