Variant report

Variant	rs431609
Chromosome Location	chr21:47334792-47334793
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47325287..47328224-chr21:47334114..47336660,2	MCF-7	breast:
2	chr21:47287743..47288527-chr21:47334754..47335348,2	MCF-7	breast:
3	chr21:47334656..47336650-chr21:47402926..47405175,2	MCF-7	breast:
4	chr21:47319454..47322116-chr21:47334445..47336417,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11089022	0.86[CEU][hapmap]
rs11089029	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11089030	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11702443	0.87[CEU][hapmap]
rs11702478	0.89[CEU][hapmap];0.88[JPT][hapmap]
rs12627257	1.00[ASW][hapmap];0.87[CEU][hapmap];0.84[GIH][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap]
rs1547240	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1736419	0.91[EUR][1000 genomes]
rs1736420	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1736422	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1736423	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1736425	0.81[EUR][1000 genomes]
rs1783075	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1883046	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1883047	0.81[EUR][1000 genomes]
rs2070437	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2075885	0.83[CEU][hapmap]
rs2075886	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2075888	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2075889	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2075890	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2075891	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2075908	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2075909	0.97[ASN][1000 genomes]
rs2150452	1.00[ASW][hapmap];0.88[MKK][hapmap]
rs2776403	0.82[EUR][1000 genomes]
rs2839015	0.90[ASW][hapmap];0.80[CHD][hapmap];1.00[LWK][hapmap]
rs2839027	0.87[CEU][hapmap]
rs2839034	0.91[ASW][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap]
rs2839042	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2839043	0.95[CEU][hapmap];0.90[CHB][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs2839044	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2839045	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2839046	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2839047	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2839048	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2839051	0.95[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs2839052	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2839060	0.95[CHB][hapmap]
rs373617	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3788219	0.87[CEU][hapmap]
rs379939	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs381083	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs386633	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs395418	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs409280	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs411868	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs413886	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs417745	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs417972	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs418241	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs418431	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs419348	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs420270	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs426594	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs435299	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs437264	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs440207	0.97[ASN][1000 genomes]
rs442400	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs444774	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs446763	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs452332	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4819162	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs4819164	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4819168	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7277160	0.97[ASN][1000 genomes]
rs7279643	0.80[EUR][1000 genomes]
rs7281225	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7281469	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7281622	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7281638	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7283556	0.80[EUR][1000 genomes]
rs7283763	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7284057	0.80[EUR][1000 genomes]
rs8132054	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs8133743	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs8134872	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[GIH][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap]
rs9975216	0.92[ASN][1000 genomes]
rs9979633	1.00[ASW][hapmap];0.88[MKK][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	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
13	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
14	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
15	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
16	nsv1062420	chr21:47311566-47347666	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
17	nsv1062386	chr21:47314890-47343364	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
18	nsv1061940	chr21:47317456-47343364	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
19	nsv1063852	chr21:47317456-47358709	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
20	nsv1060235	chr21:47317456-47360544	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs431609	COL18A1	cis	parietal	SCAN
rs431609	TFF1	cis	cerebellum	SCAN
rs431609	HOXB8	trans	cerebellum	SCAN
rs431609	COL6A1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47308000-47343000	Weak transcription	Right Atrium	heart
2	chr21:47313200-47335600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr21:47321800-47337800	Weak transcription	Primary T cells from cord blood	blood
4	chr21:47322200-47335200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr21:47325600-47335600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr21:47327000-47335600	Weak transcription	Fetal Thymus	thymus
7	chr21:47330600-47335600	Weak transcription	Adipose Nuclei	Adipose
8	chr21:47330600-47335600	Weak transcription	Fetal Lung	lung
9	chr21:47330800-47342200	Weak transcription	Brain Hippocampus Middle	brain
10	chr21:47332200-47334800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr21:47332600-47335600	Weak transcription	Spleen	Spleen
12	chr21:47333600-47351600	Weak transcription	Gastric	stomach
13	chr21:47333800-47338800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr21:47334200-47335000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr21:47334200-47335400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr21:47334200-47336600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr21:47334200-47338000	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr21:47334400-47335200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr21:47334400-47340000	Weak transcription	Thymus	Thymus
20	chr21:47334600-47335000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr21:47334600-47335800	Enhancers	HMEC	breast

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