Variant report

Variant	rs34497559
Chromosome Location	chr21:46669733-46669734
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46664716..46666767-chr21:46668227..46671842,4	K562	blood:
2	chr21:46605915..46607896-chr21:46668846..46670608,2	K562	blood:
3	chr21:46492783..46494831-chr21:46669105..46671961,2	K562	blood:
4	chr21:46653586..46657139-chr21:46668984..46671071,3	K562	blood:

Variant related genes	Relation type
ENSG00000268856	Chromatin interaction
ENSG00000182586	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000235374	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10470245	0.92[ASN][1000 genomes]
rs10470247	0.86[ASN][1000 genomes]
rs10470258	0.88[ASN][1000 genomes]
rs1075788	0.92[ASN][1000 genomes]
rs12626188	0.93[ASN][1000 genomes]
rs1304487	0.91[ASN][1000 genomes]
rs1304488	0.92[ASN][1000 genomes]
rs13047104	0.93[ASN][1000 genomes]
rs13047598	0.91[ASN][1000 genomes]
rs13048789	0.92[ASN][1000 genomes]
rs13049049	0.92[ASN][1000 genomes]
rs13049337	0.92[ASN][1000 genomes]
rs13050359	0.92[ASN][1000 genomes]
rs13052312	0.92[ASN][1000 genomes]
rs1999333	0.93[ASN][1000 genomes]
rs1999335	0.93[ASN][1000 genomes]
rs2330011	0.91[ASN][1000 genomes]
rs2330012	0.92[ASN][1000 genomes]
rs2838825	0.84[ASN][1000 genomes]
rs2838826	0.90[ASN][1000 genomes]
rs2838827	0.91[ASN][1000 genomes]
rs2838828	0.92[ASN][1000 genomes]
rs2838829	0.92[ASN][1000 genomes]
rs2838831	0.92[ASN][1000 genomes]
rs2838832	0.92[ASN][1000 genomes]
rs2838833	0.92[ASN][1000 genomes]
rs2838834	0.92[ASN][1000 genomes]
rs2838837	0.92[ASN][1000 genomes]
rs2838839	0.91[ASN][1000 genomes]
rs2838840	0.91[ASN][1000 genomes]
rs2838842	0.93[ASN][1000 genomes]
rs2838843	0.93[ASN][1000 genomes]
rs2838844	0.93[ASN][1000 genomes]
rs2838845	0.93[ASN][1000 genomes]
rs2838848	0.94[ASN][1000 genomes]
rs2838849	0.94[ASN][1000 genomes]
rs2838850	0.93[ASN][1000 genomes]
rs2877018	0.92[ASN][1000 genomes]
rs2877019	0.90[ASN][1000 genomes]
rs2877020	0.92[ASN][1000 genomes]
rs34101026	0.92[ASN][1000 genomes]
rs34818688	0.91[ASN][1000 genomes]
rs35560973	0.91[ASN][1000 genomes]
rs35997212	0.90[ASN][1000 genomes]
rs4818768	0.92[ASN][1000 genomes]
rs4819038	0.92[ASN][1000 genomes]
rs4819039	0.92[ASN][1000 genomes]
rs4819040	0.91[ASN][1000 genomes]
rs4819041	0.91[ASN][1000 genomes]
rs4819042	0.92[ASN][1000 genomes]
rs4819043	0.90[ASN][1000 genomes]
rs4819044	0.92[ASN][1000 genomes]
rs4819045	0.92[ASN][1000 genomes]
rs4819046	0.92[ASN][1000 genomes]
rs4819047	0.92[ASN][1000 genomes]
rs4819048	0.90[ASN][1000 genomes]
rs4819049	0.92[ASN][1000 genomes]
rs58644915	0.93[ASN][1000 genomes]
rs7275468	0.91[ASN][1000 genomes]
rs7275870	0.93[ASN][1000 genomes]
rs7275874	0.93[ASN][1000 genomes]
rs7276103	0.89[ASN][1000 genomes]
rs7279011	0.91[ASN][1000 genomes]
rs7279182	0.91[ASN][1000 genomes]
rs7283915	0.91[ASN][1000 genomes]
rs8126930	0.92[ASN][1000 genomes]
rs8130285	0.93[ASN][1000 genomes]
rs8131143	0.93[ASN][1000 genomes]
rs8131476	0.91[ASN][1000 genomes]
rs8132387	0.92[ASN][1000 genomes]
rs8133045	0.92[ASN][1000 genomes]
rs8133153	0.91[ASN][1000 genomes]
rs8134392	0.92[ASN][1000 genomes]
rs9753962	0.92[ASN][1000 genomes]
rs9753963	0.92[ASN][1000 genomes]
rs9753987	0.92[ASN][1000 genomes]
rs9754134	0.92[ASN][1000 genomes]
rs9974628	0.89[ASN][1000 genomes]
rs9977178	0.92[ASN][1000 genomes]
rs9980676	0.92[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	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1059771	chr21:46561482-46830602	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv544481	chr21:46561482-46830602	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1063943	chr21:46571988-46819424	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv544482	chr21:46571988-46819424	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv1064859	chr21:46571988-46830602	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	nsv544483	chr21:46571988-46830602	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS 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 target site	51 gene(s)	inside rSNPs	diseases
8	nsv1061691	chr21:46572641-46831862	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer 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 miRNA target site	51 gene(s)	inside rSNPs	diseases
9	nsv544484	chr21:46572641-46831862	Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
10	nsv587839	chr21:46580370-46837709	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
11	nsv587840	chr21:46580370-46839904	Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
12	nsv916959	chr21:46585681-46831845	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
13	nsv1063721	chr21:46610599-46907894	Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
14	nsv1059779	chr21:46611859-46891352	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
15	nsv544485	chr21:46611859-46891352	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
16	nsv1059805	chr21:46618210-46736943	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv913999	chr21:46636844-46765251	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
18	nsv587842	chr21:46641017-46670752	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
19	nsv914000	chr21:46647078-46765251	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
20	nsv914001	chr21:46647078-46944113	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
21	nsv914002	chr21:46655638-46945024	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
22	nsv1057807	chr21:46656346-47077374	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs34497559	LOC642852	cis	brain	BrainEAC
rs34497559	LOC642852	cis	frontal cortex	BrainEAC
rs34497559	POFUT2	cis	brain	BrainEAC
rs34497559	LOC642852	cis	temporal cortex	BrainEAC

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46668800-46669800	Enhancers	Spleen	Spleen
2	chr21:46669000-46672600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr21:46669000-46683400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr21:46669200-46670200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr21:46669200-46670400	Enhancers	Colon Smooth Muscle	Colon
6	chr21:46669200-46672800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr21:46669200-46674600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr21:46669200-46677000	Weak transcription	Left Ventricle	heart
9	chr21:46669200-46706600	Weak transcription	Right Atrium	heart
10	chr21:46669400-46670800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr21:46669400-46670800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr21:46669400-46671000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr21:46669400-46671600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr21:46669400-46673200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr21:46669400-46673200	Weak transcription	Osteobl	bone

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