Variant report

Variant	rs1014446
Chromosome Location	chr21:47279147-47279148
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47273743..47277318-chr21:47278622..47280436,3	K562	blood:

Variant related genes	Relation type
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10854472	0.96[ASN][1000 genomes]
rs11089024	0.92[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs11089027	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12481867	0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.96[ASN][1000 genomes]
rs12481913	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12481970	0.95[ASN][1000 genomes]
rs12481977	0.96[ASN][1000 genomes]
rs12482010	0.95[ASN][1000 genomes]
rs12482094	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.96[ASN][1000 genomes]
rs12482377	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12482750	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12482853	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17351419	0.96[ASN][1000 genomes]
rs17351433	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2065334	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2183595	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2183596	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2838973	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2838974	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2838976	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2838982	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2838989	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2838991	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2838992	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2838993	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2838994	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2839003	0.83[ASN][1000 genomes]
rs2839004	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2839005	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2839009	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2839013	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2839014	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2839026	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2839029	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839032	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3367	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs35781238	0.81[ASN][1000 genomes]
rs3788208	0.93[ASN][1000 genomes]
rs3788209	0.96[ASN][1000 genomes]
rs3788211	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3788215	0.94[ASN][1000 genomes]
rs3788216	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3788220	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3788224	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788227	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3920695	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs4434082	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs4818801	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4818802	0.96[ASN][1000 genomes]
rs4818803	0.96[ASN][1000 genomes]
rs4818805	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819154	0.95[ASN][1000 genomes]
rs4819155	0.96[ASN][1000 genomes]
rs4819156	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4819157	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs55780126	0.83[ASN][1000 genomes]
rs55856400	0.96[ASN][1000 genomes]
rs55875620	0.83[ASN][1000 genomes]
rs55912352	0.96[ASN][1000 genomes]
rs55927540	0.93[ASN][1000 genomes]
rs57688476	0.91[ASN][1000 genomes]
rs61063225	0.94[ASN][1000 genomes]
rs61276251	0.91[ASN][1000 genomes]
rs62211883	0.96[ASN][1000 genomes]
rs62211885	0.96[ASN][1000 genomes]
rs62211886	0.96[ASN][1000 genomes]
rs62211895	0.96[ASN][1000 genomes]
rs62211925	0.96[ASN][1000 genomes]
rs62211926	0.96[ASN][1000 genomes]
rs62214604	0.83[ASN][1000 genomes]
rs62214608	0.93[ASN][1000 genomes]
rs66523344	0.96[ASN][1000 genomes]
rs67055992	0.96[ASN][1000 genomes]
rs67878041	0.96[ASN][1000 genomes]
rs7280173	0.96[ASN][1000 genomes]
rs8127369	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs8127428	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs882668	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs882669	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914241	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs9306139	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs9637208	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs964975	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9977908	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9978740	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9983770	0.96[ASN][1000 genomes]
rs9984668	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
4	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
6	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
8	nsv428043	chr21:47179244-47471971	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a
9	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
10	nsv914078	chr21:47218744-47311686	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
11	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
12	esv2756755	chr21:47243032-47319768	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
13	esv2758821	chr21:47243032-47319768	Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
14	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a
15	nsv914080	chr21:47265786-47311686	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
16	nsv914081	chr21:47265786-47320805	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
17	nsv914082	chr21:47265786-47338007	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
18	nsv914083	chr21:47265786-47453954	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
19	esv2072832	chr21:47279000-47279437	Genic enhancers Weak transcription Strong transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
20	esv3392377	chr21:47279097-47279316	Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1014446	PCBP3	cis	cerebellum	SCAN
rs1014446	COL18A1	cis	parietal	SCAN
rs1014446	COL6A1	cis	cerebellum	SCAN
rs1014446	FTCD	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47265800-47282000	Weak transcription	Primary T cells from cord blood	blood
2	chr21:47266800-47300600	Weak transcription	Right Atrium	heart
3	chr21:47272400-47282000	Strong transcription	Thymus	Thymus
4	chr21:47273200-47289400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr21:47273800-47299200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr21:47275200-47284200	Weak transcription	HSMMtube	muscle
7	chr21:47275400-47281200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr21:47275800-47281000	Weak transcription	Adipose Nuclei	Adipose
9	chr21:47275800-47284200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr21:47277200-47280600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr21:47277400-47281000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr21:47278400-47279600	Strong transcription	Fetal Thymus	thymus
13	chr21:47278400-47282800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr21:47278400-47283000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr21:47278800-47279800	Enhancers	Liver	Liver
16	chr21:47279000-47279200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr21:47279000-47279200	Bivalent Enhancer	HepG2	liver
18	chr21:47279000-47279600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr21:47279000-47280200	Strong transcription	Spleen	Spleen
20	chr21:47279000-47280800	Bivalent Enhancer	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links