Variant report

Variant	rs9977242
Chromosome Location	chr21:47354601-47354602
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr21:47354580-47354730	HBMEC	blood vessel:	n/a	chr21:47354624-47354642 chr21:47354642-47354655 chr21:47354634-47354652 chr21:47354619-47354640
2	CTCF	chr21:47354513-47354775	K562	blood:	n/a	chr21:47354624-47354642 chr21:47354642-47354655 chr21:47354634-47354652 chr21:47354619-47354640
3	CTCF	chr21:47354495-47354767	K562	blood:	n/a	chr21:47354624-47354642 chr21:47354642-47354655 chr21:47354634-47354652 chr21:47354619-47354640
4	CTCF	chr21:47354480-47354630	GM12872	blood:	n/a	n/a
5	CTCF	chr21:47354560-47354710	GM12873	blood:	n/a	chr21:47354624-47354642 chr21:47354642-47354655 chr21:47354634-47354652 chr21:47354619-47354640
6	CTCF	chr21:47354560-47354710	WERI-Rb-1	eye:	n/a	chr21:47354624-47354642 chr21:47354642-47354655 chr21:47354634-47354652 chr21:47354619-47354640
7	CTCF	chr21:47354567-47354701	K562	blood:	n/a	chr21:47354624-47354642 chr21:47354642-47354655 chr21:47354634-47354652 chr21:47354619-47354640
8	CTCF	chr21:47354580-47354730	HepG2	liver:	n/a	chr21:47354624-47354642 chr21:47354642-47354655 chr21:47354634-47354652 chr21:47354619-47354640
9	CTCF	chr21:47354560-47354710	HEK293	kidney:	n/a	chr21:47354624-47354642 chr21:47354642-47354655 chr21:47354634-47354652 chr21:47354619-47354640
10	RAD21	chr21:47354532-47354684	K562	blood:	n/a	chr21:47354636-47354646 chr21:47354622-47354641 chr21:47354632-47354651 chr21:47354624-47354636
11	CTCF	chr21:47354560-47354710	GM12865	blood:	n/a	chr21:47354624-47354642 chr21:47354642-47354655 chr21:47354634-47354652 chr21:47354619-47354640
12	CTCF	chr21:47354540-47354690	NB4	blood:	n/a	chr21:47354624-47354642 chr21:47354642-47354655 chr21:47354634-47354652 chr21:47354619-47354640
13	CTCF	chr21:47354540-47354690	K562	blood:	n/a	chr21:47354624-47354642 chr21:47354642-47354655 chr21:47354634-47354652 chr21:47354619-47354640

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47353624..47355252-chr21:47356689..47359640,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268040	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10222081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10470261	1.00[ASN][1000 genomes]
rs16978692	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075887	0.80[ASN][1000 genomes]
rs2075907	0.92[ASN][1000 genomes]
rs2776402	0.94[ASN][1000 genomes]
rs2839065	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839066	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839067	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839068	1.00[ASN][1000 genomes]
rs2839069	1.00[ASN][1000 genomes]
rs2839071	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3746990	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3746991	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788229	0.94[ASN][1000 genomes]
rs3788232	0.98[ASN][1000 genomes]
rs3788235	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3788239	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs379493	0.94[ASN][1000 genomes]
rs379501	0.94[ASN][1000 genomes]
rs3827269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs446403	0.81[ASN][1000 genomes]
rs58139084	0.94[ASN][1000 genomes]
rs59605057	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60282450	0.94[ASN][1000 genomes]
rs60911498	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61639161	0.84[ASN][1000 genomes]
rs7276479	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7276791	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7277199	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306145	1.00[ASN][1000 genomes]
rs9975850	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9983166	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9983756	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	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
16	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
17	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
18	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
19	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
20	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
21	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47340000-47354800	Weak transcription	Primary T cells from cord blood	blood
2	chr21:47353600-47356600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr21:47353600-47357000	ZNF genes & repeats	Fetal Thymus	thymus
4	chr21:47353600-47357800	ZNF genes & repeats	Brain Hippocampus Middle	brain
5	chr21:47353800-47357000	ZNF genes & repeats	Spleen	Spleen
6	chr21:47353800-47357400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr21:47354000-47355200	ZNF genes & repeats	Fetal Stomach	stomach
8	chr21:47354400-47356800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr21:47354400-47356800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr21:47354600-47355400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
11	chr21:47354600-47356400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
12	chr21:47354600-47356400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr21:47354600-47356600	ZNF genes & repeats	Thymus	Thymus
14	chr21:47354600-47357000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr21:47354600-47357000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
16	chr21:47354600-47357200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
17	chr21:47354600-47357400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr21:47354600-47357400	ZNF genes & repeats	Fetal Muscle Leg	muscle
19	chr21:47354600-47362400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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