Variant report

Variant	rs420270
Chromosome Location	chr21:47369190-47369191
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47368443..47370722-chr21:47372647..47374224,2	K562	blood:

Extended variants
information (count: 100 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11089022	0.86[CEU][hapmap]
rs11089030	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11700515	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11700554	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11700659	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11700719	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11700929	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11702443	0.87[CEU][hapmap]
rs11702467	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11702478	0.89[CEU][hapmap];0.83[JPT][hapmap]
rs11702503	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11702616	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11702691	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12627257	0.83[ASW][hapmap];0.87[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs1547240	0.85[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs1736419	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1736420	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1736422	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1736423	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1736425	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1783075	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1883046	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1883047	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2070437	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2075885	0.83[CEU][hapmap]
rs2075908	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2075909	0.84[ASN][1000 genomes]
rs2150452	0.83[ASW][hapmap]
rs2150459	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2776403	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2839027	0.87[CEU][hapmap]
rs2839042	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs2839043	0.96[CEU][hapmap];0.90[CHB][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs2839044	0.85[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs2839045	0.95[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs2839046	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2839048	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2839051	0.91[CEU][hapmap];0.83[CHB][hapmap];0.87[TSI][hapmap]
rs2839052	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2839060	0.95[CHB][hapmap]
rs373617	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3788219	0.87[CEU][hapmap]
rs379939	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs381083	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs386633	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs395418	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs409280	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs411868	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs413886	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs417745	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs417972	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs418241	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs418431	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs419348	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs426594	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs431609	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs435299	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs437264	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs440207	0.84[ASN][1000 genomes]
rs442400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs444774	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs446763	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs452877	0.84[AMR][1000 genomes]
rs4819162	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs4819164	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs4819168	0.85[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7277160	0.84[ASN][1000 genomes]
rs7277877	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7278816	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7279643	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7281469	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs7281573	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7282661	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7283763	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs8132054	0.85[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs8133743	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs8134872	0.83[ASW][hapmap];0.83[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs9975216	0.88[ASN][1000 genomes]
rs9979633	0.83[ASW][hapmap]

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	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
11	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
12	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
13	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
14	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
15	nsv914085	chr21:47342116-47433055	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
16	esv1848879	chr21:47343462-47455584	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
17	nsv914086	chr21:47352625-47445184	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a
18	nsv914087	chr21:47352625-47453954	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
19	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
20	nsv914088	chr21:47358915-47419012	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs420270	COL18A1	cis	parietal	SCAN
rs420270	HOXB8	trans	cerebellum	SCAN
rs420270	HSF2BP	cis	cerebellum	SCAN
rs420270	COL6A1	cis	cerebellum	SCAN
rs420270	TFF1	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47361000-47370600	Weak transcription	Thymus	Thymus
2	chr21:47361200-47370000	Weak transcription	Spleen	Spleen
3	chr21:47367400-47373000	Weak transcription	Right Atrium	heart
4	chr21:47368600-47369400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr21:47368600-47369800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr21:47368600-47371000	Bivalent Enhancer	Placenta	Placenta
7	chr21:47368800-47369200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr21:47368800-47369200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
9	chr21:47368800-47369200	Flanking Bivalent TSS/Enh	K562	blood
10	chr21:47368800-47370600	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr21:47369000-47369200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr21:47369000-47369400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr21:47369000-47369400	Enhancers	HSMMtube	muscle
14	chr21:47369000-47369800	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr21:47369000-47369800	Enhancers	Adipose Nuclei	Adipose
16	chr21:47369000-47369800	Weak transcription	Right Ventricle	heart
17	chr21:47369000-47369800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
18	chr21:47369000-47370200	Weak transcription	Lung	lung
19	chr21:47369000-47370400	Bivalent Enhancer	NHEK	skin
20	chr21:47369000-47371000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr21:47369000-47373000	Weak transcription	Left Ventricle	heart

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