Variant report

Variant	rs4456788
Chromosome Location	chr21:45616324-45616325
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	RXRA	chr21:45616140-45616440	GM12878	blood:	n/a	n/a
2	TAF1	chr21:45616151-45616510	GM12878	blood:	n/a	n/a
3	SPI1	chr21:45616014-45616669	HL-60	blood:	n/a	chr21:45616349-45616358 chr21:45616348-45616361 chr21:45616350-45616357
4	MAX	chr21:45616001-45616692	K562	blood:	n/a	chr21:45616217-45616226 chr21:45616213-45616222 chr21:45616215-45616225 chr21:45616214-45616224 chr21:45616259-45616268 chr21:45616213-45616228
5	YY1	chr21:45616094-45616594	GM12878	blood:	n/a	n/a
6	POLR2A	chr21:45615804-45616806	GM12878	blood:	n/a	n/a
7	POLR2A	chr21:45615973-45616758	GM15510	blood:	n/a	n/a
8	RUNX3	chr21:45615867-45616637	GM12878	blood:	n/a	n/a
9	REST	chr21:45616230-45616441	PANC-1	pancreas:	n/a	chr21:45616369-45616378 chr21:45616263-45616283
10	RELA	chr21:45615995-45616575	GM19099	blood:	n/a	n/a
11	PAX5	chr21:45615825-45616771	GM12878	blood:	n/a	chr21:45616279-45616288
12	POLR2A	chr21:45615908-45616661	GM12891	blood:	n/a	n/a
13	CUX1	chr21:45616153-45616793	K562	blood:	n/a	n/a
14	POLR2A	chr21:45615997-45616709	GM19099	blood:	n/a	n/a
15	POLR2A	chr21:45615978-45616648	GM18505	blood:	n/a	n/a
16	MAX	chr21:45616135-45616411	K562	blood:	n/a	chr21:45616217-45616226 chr21:45616213-45616222 chr21:45616215-45616225 chr21:45616214-45616224 chr21:45616259-45616268 chr21:45616213-45616228
17	BATF	chr21:45616055-45616561	GM12878	blood:	n/a	n/a
18	REST	chr21:45616149-45616529	PFSK-1	brain:	n/a	chr21:45616369-45616378 chr21:45616263-45616283
19	SPI1	chr21:45616147-45616542	GM12878	blood:	n/a	chr21:45616349-45616358 chr21:45616348-45616361 chr21:45616350-45616357
20	SP1	chr21:45616014-45616611	GM12878	blood:	n/a	n/a
21	ELF1	chr21:45616101-45616609	K562	blood:	n/a	chr21:45616347-45616360 chr21:45616349-45616360
22	USF1	chr21:45616032-45616486	K562	blood:	n/a	n/a
23	CREB1	chr21:45616028-45616574	K562	blood:	n/a	n/a
24	RUNX3	chr21:45615756-45616764	GM12878	blood:	n/a	n/a
25	TCF3	chr21:45616028-45616520	GM12878	blood:	n/a	chr21:45616493-45616502 chr21:45616490-45616505
26	POLR2A	chr21:45615955-45616687	GM18526	blood:	n/a	n/a
27	POLR2A	chr21:45615849-45616878	GM12892	blood:	n/a	n/a
28	ATF3	chr21:45616046-45616449	K562	blood:	n/a	n/a
29	RFX5	chr21:45616150-45616632	GM12878	blood:	n/a	n/a
30	GATA3	chr21:45615969-45616846	MCF-7	breast:	n/a	chr21:45616563-45616580
31	BATF	chr21:45616096-45616518	GM12878	blood:	n/a	n/a
32	EBF1	chr21:45615806-45616654	GM12878	blood:	n/a	n/a
33	POU2F2	chr21:45616087-45616715	GM12891	blood:	n/a	n/a
34	NRF1	chr21:45616188-45616562	GM12878	blood:	n/a	n/a
35	JUN	chr21:45615817-45617579	K562	blood:	n/a	n/a
36	POLR2A	chr21:45615881-45616888	PBDE	blood:	n/a	n/a
37	MAZ	chr21:45616074-45616763	K562	blood:	n/a	chr21:45616217-45616226 chr21:45616213-45616222 chr21:45616215-45616225 chr21:45616214-45616224 chr21:45616259-45616268 chr21:45616213-45616228
38	POU2F2	chr21:45616097-45616490	GM12878	blood:	n/a	n/a
39	PBX3	chr21:45616203-45616708	GM12878	blood:	n/a	n/a
40	CHD2	chr21:45615929-45616813	GM12878	blood:	n/a	chr21:45616323-45616333
41	ZMIZ1	chr21:45616152-45616693	K562	blood:	n/a	n/a
42	REST	chr21:45616067-45616616	PFSK-1	brain:	n/a	chr21:45616369-45616378 chr21:45616263-45616283 chr21:45616099-45616113 chr21:45616101-45616111
43	REST	chr21:45616050-45616717	PFSK-1	brain:	n/a	chr21:45616369-45616378 chr21:45616263-45616283 chr21:45616099-45616113 chr21:45616101-45616111
44	YY1	chr21:45615977-45616447	GM12878	blood:	n/a	n/a
45	REST	chr21:45616132-45616553	GM12878	blood:	n/a	chr21:45616369-45616378 chr21:45616263-45616283
46	PML	chr21:45615478-45616718	GM12878	blood:	n/a	n/a
47	ATF2	chr21:45615953-45616749	GM12878	blood:	n/a	n/a
48	IRF4	chr21:45615993-45616649	GM12878	blood:	n/a	n/a
49	SPI1	chr21:45616144-45616553	GM12891	blood:	n/a	chr21:45616349-45616358 chr21:45616348-45616361 chr21:45616350-45616357
50	MYC	chr21:45615996-45616667	NB4	blood:	n/a	chr21:45616217-45616226 chr21:45616213-45616222 chr21:45616215-45616225 chr21:45616214-45616224 chr21:45616259-45616268 chr21:45616213-45616228

No.	Distal block	Cell Line	Cell type
1	chr21:45565762..45568425-chr21:45616246..45618901,2	MCF-7	breast:
2	chr21:45593299..45595142-chr21:45615478..45617030,2	MCF-7	breast:
3	chr21:45574118..45574672-chr21:45616064..45616668,2	MCF-7	breast:
4	chr21:45557116..45559735-chr21:45615528..45618206,3	MCF-7	breast:
5	chr21:45616221..45617876-chr21:45625272..45628231,2	K562	blood:
6	chr21:45615502..45617869-chr21:45667459..45670293,2	K562	blood:
7	chr21:45615955..45617029-chr21:45660335..45661089,5	MCF-7	breast:
8	chr21:45586838..45589344-chr21:45614842..45616536,2	MCF-7	breast:
9	chr21:45610715..45617377-chr21:45717031..45721978,7	MCF-7	breast:
10	chr21:45568616..45570755-chr21:45615083..45617675,2	K562	blood:
11	chr21:45609075..45610927-chr21:45615037..45616803,2	K562	blood:
12	chr21:45615189..45618434-chr21:45625221..45628569,5	MCF-7	breast:
13	chr21:45614676..45619255-chr21:45657692..45665676,14	MCF-7	breast:
14	chr21:45595676..45596715-chr21:45615636..45617128,25	MCF-7	breast:
15	chr21:45595680..45596514-chr21:45615830..45617060,14	MCF-7	breast:
16	chr21:45612993..45620081-chr21:45620303..45625017,17	MCF-7	breast:
17	chr21:45567927..45569479-chr21:45614833..45617390,2	K562	blood:
18	chr21:45607137..45608941-chr21:45615370..45617109,2	K562	blood:
19	chr21:45570114..45570951-chr21:45616167..45617027,2	MCF-7	breast:
20	chr21:45595676..45596652-chr21:45615636..45617063,9	MCF-7	breast:
21	chr21:45615955..45617029-chr21:45660387..45661089,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232124	TF binding region
ENSG00000232124	Chromatin interaction
ENSG00000160223	Chromatin interaction
ENSG00000267913	Chromatin interaction
ENSG00000232698	Chromatin interaction
ENSG00000141959	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11089118	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2070551	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2070552	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838516	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838517	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838519	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2838520	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838521	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2876932	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35405602	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3746958	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3804031	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3804032	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4317019	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4380337	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4635612	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7276302	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7282490	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs743478	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs743479	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs762421	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762422	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762423	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127691	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8134436	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv1064420	chr21:45460089-45814986	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv544472	chr21:45460089-45814986	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv432155	chr21:45479055-45772388	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv913894	chr21:45508561-45627976	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv913897	chr21:45528919-45640139	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv1825445	chr21:45535566-45754936	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
9	esv1817474	chr21:45540607-45773102	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
10	nsv533679	chr21:45551026-45768578	Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription 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	64 gene(s)	inside rSNPs	diseases
11	nsv913898	chr21:45555079-45941566	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	74 gene(s)	inside rSNPs	diseases
12	nsv428042	chr21:45560437-45848190	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
13	nsv1065479	chr21:45571324-45617878	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv913900	chr21:45577102-45640139	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
15	esv3411301	chr21:45609579-45620771	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
16	esv3455479	chr21:45609616-45620726	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
17	esv3455480	chr21:45609633-45620722	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
18	nsv913901	chr21:45615741-45665330	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS 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	21 gene(s)	inside rSNPs	diseases
19	nsv913902	chr21:45615741-45709153	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45610800-45616600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr21:45610800-45617600	Enhancers	Placenta	Placenta
3	chr21:45612200-45617200	Enhancers	Fetal Muscle Leg	muscle
4	chr21:45612400-45616400	Weak transcription	Esophagus	oesophagus
5	chr21:45612600-45616400	Weak transcription	Right Ventricle	heart
6	chr21:45612800-45617400	Enhancers	Primary hematopoietic stem cells	blood
7	chr21:45613200-45617000	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr21:45613600-45617200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr21:45613600-45617400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr21:45613600-45617400	Enhancers	Primary B cells from peripheral blood	blood
11	chr21:45614000-45617000	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr21:45614000-45617200	Enhancers	GM12878-XiMat	blood
13	chr21:45614000-45617600	Enhancers	Primary B cells from cord blood	blood
14	chr21:45614400-45617400	Weak transcription	Brain Angular Gyrus	brain
15	chr21:45614600-45616400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr21:45614600-45616600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr21:45614800-45616400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr21:45614800-45616400	Weak transcription	Right Atrium	heart
19	chr21:45614800-45622400	Weak transcription	Pancreas	Pancrea
20	chr21:45615000-45617200	Weak transcription	Colonic Mucosa	Colon
21	chr21:45615000-45623200	Weak transcription	Brain Hippocampus Middle	brain
22	chr21:45615400-45616400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
23	chr21:45615400-45616800	Weak transcription	Brain Anterior Caudate	brain
24	chr21:45615400-45622200	Weak transcription	Fetal Lung	lung
25	chr21:45615600-45616800	Enhancers	Primary T cells from cord blood	blood
26	chr21:45615600-45616800	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr21:45615600-45616800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr21:45615600-45617000	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr21:45615600-45617000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr21:45615600-45617000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr21:45615600-45617000	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr21:45615600-45617200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr21:45615600-45617200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr21:45615600-45617400	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr21:45615600-45617800	Enhancers	Fetal Thymus	thymus
36	chr21:45615800-45616400	Enhancers	K562	blood
37	chr21:45615800-45616800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr21:45615800-45616800	Enhancers	Spleen	Spleen
39	chr21:45615800-45617000	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr21:45615800-45617200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr21:45615800-45617400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr21:45615800-45617400	Enhancers	Brain Substantia Nigra	brain
43	chr21:45615800-45617600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr21:45615800-45617800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr21:45616000-45616400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr21:45616000-45616600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
47	chr21:45616000-45616600	Enhancers	Duodenum Mucosa	Duodenum
48	chr21:45616000-45616600	Enhancers	Lung	lung
49	chr21:45616000-45616600	Enhancers	Stomach Mucosa	stomach
50	chr21:45616000-45616800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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