Variant report

Variant	rs4865809
Chromosome Location	chr5:53504764-53504765
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10051537	0.93[CHB][hapmap];0.86[YRI][hapmap];0.84[ASN][1000 genomes]
rs10076217	0.91[ASN][1000 genomes]
rs1345815	0.93[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.91[ASN][1000 genomes]
rs154020	0.86[CHB][hapmap];0.90[AMR][1000 genomes]
rs156830	0.93[CHB][hapmap]
rs16882414	0.81[ASW][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.83[YRI][hapmap]
rs16882451	0.86[CHB][hapmap];0.96[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs202168	0.93[CHB][hapmap];0.89[MEX][hapmap]
rs2407404	0.93[CHB][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs244643	0.93[CHB][hapmap]
rs2547538	0.86[CHB][hapmap]
rs25853	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs26608	0.93[CHB][hapmap]
rs26609	0.93[CHB][hapmap];0.84[MEX][hapmap]
rs26775	0.93[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes]
rs26776	0.84[AMR][1000 genomes]
rs277323	0.87[CHB][hapmap];0.84[MEX][hapmap]
rs277329	0.87[CHB][hapmap];0.89[MEX][hapmap]
rs277330	0.93[CHB][hapmap]
rs27776	0.87[CHB][hapmap];0.90[AMR][1000 genomes]
rs278065	0.93[CHB][hapmap];0.89[MEX][hapmap]
rs27897	0.93[CHB][hapmap]
rs279743	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs279744	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs28033	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs35006	0.86[CHB][hapmap]
rs3797254	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs3797255	0.93[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs3843452	1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[YRI][hapmap];0.88[ASN][1000 genomes]
rs464888	0.87[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4865807	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4865808	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.99[ASN][1000 genomes]
rs682103	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs6866862	0.93[CHB][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6866870	0.93[CHB][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs700915	0.93[CHB][hapmap]
rs981713	0.82[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats 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 miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv881265	chr5:53305742-53504764	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv880619	chr5:53305742-53525671	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv881616	chr5:53305742-53639975	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv881018	chr5:53305742-53744849	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
7	nsv880734	chr5:53305742-53770217	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv881161	chr5:53305742-53815495	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv881600	chr5:53305742-53823285	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
10	nsv598176	chr5:53311502-53739530	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
11	nsv880773	chr5:53311918-53815495	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1024303	chr5:53317896-53788276	Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
13	nsv1029224	chr5:53317896-53812899	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
14	nsv949098	chr5:53317990-53816782	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
15	nsv1020517	chr5:53324930-53759046	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
16	nsv1017768	chr5:53326385-53752165	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
17	nsv1032352	chr5:53327170-53762973	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
18	nsv598177	chr5:53333477-53755208	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
19	nsv881056	chr5:53368869-53744849	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
20	nsv881408	chr5:53386267-53815495	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
21	nsv1031072	chr5:53490130-53698866	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
22	nsv524694	chr5:53504764-53509186	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4865809	ANKRD55	cis	cerebellum	SCAN
rs4865809	HSPB3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53489400-53506600	Weak transcription	Aorta	Aorta
2	chr5:53498000-53509200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:53498400-53506600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:53498400-53510000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:53501400-53508200	Weak transcription	Pancreas	Pancrea
6	chr5:53502200-53507000	Weak transcription	Liver	Liver
7	chr5:53503400-53505200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:53503600-53507000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:53503600-53507000	Weak transcription	Left Ventricle	heart
10	chr5:53504000-53507000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:53504000-53507000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr5:53504000-53507800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:53504000-53508000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr5:53504000-53508200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr5:53504000-53509200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:53504200-53506600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:53504200-53506800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:53504200-53508000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:53504200-53508000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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