Variant report

Variant	rs559480
Chromosome Location	chr21:44781984-44781985
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr21:44781972-44782549	GM12878	blood:	n/a	n/a
2	POLR2A	chr21:44781552-44782125	GM12878	blood:	n/a	n/a
3	RELA	chr21:44781556-44782672	GM18505	blood:	n/a	n/a
4	CEBPB	chr21:44781851-44782473	IMR90	lung:	n/a	n/a
5	POLR2A	chr21:44780763-44782665	GM19193	blood:	n/a	n/a
6	POLR2A	chr21:44780975-44782044	GM12892	blood:	n/a	n/a
7	RUNX3	chr21:44781571-44781996	GM12878	blood:	n/a	n/a
8	PAX5	chr21:44781930-44782533	GM12878	blood:	n/a	n/a
9	ELF1	chr21:44781362-44782094	GM12878	blood:	n/a	n/a
10	RAD21	chr21:44781042-44782697	IMR90	lung:	n/a	n/a
11	MTA3	chr21:44781622-44782003	GM12878	blood:	n/a	n/a
12	EP300	chr21:44781956-44782950	SK-N-SH	brain:	n/a	chr21:44782350-44782366
13	MXI1	chr21:44781973-44782929	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr21:44781817-44782004	GM12878	blood:	n/a	n/a
15	POLR2A	chr21:44780909-44782682	GM12892	blood:	n/a	n/a
16	POLR2A	chr21:44779653-44782706	IMR90	lung:	n/a	n/a
17	PAX5	chr21:44781572-44782700	GM12878	blood:	n/a	n/a
18	POLR2A	chr21:44781087-44782675	GM19099	blood:	n/a	n/a
19	POLR2A	chr21:44781427-44782057	ProgFib	skin:	n/a	n/a
20	POLR2A	chr21:44780985-44782654	GM18951	blood:	n/a	n/a
21	MAZ	chr21:44780514-44782772	IMR90	lung:	n/a	n/a
22	POLR2A	chr21:44781390-44782640	GM12878	blood:	n/a	n/a
23	STAT5A	chr21:44781832-44782272	GM12878	blood:	n/a	n/a
24	POLR2A	chr21:44780840-44782546	Raji	blood:	n/a	n/a
25	POLR2A	chr21:44780908-44782650	GM12892	blood:	n/a	n/a
26	POLR2A	chr21:44781055-44782614	GM15510	blood:	n/a	n/a
27	POLR2A	chr21:44781557-44782042	GM12892	blood:	n/a	n/a
28	POLR2A	chr21:44780913-44782666	GM18505	blood:	n/a	n/a
29	POLR2A	chr21:44781156-44782631	GM18526	blood:	n/a	n/a
30	POU2F2	chr21:44781597-44782404	GM12878	blood:	n/a	n/a
31	POLR2A	chr21:44781256-44782622	GM12878	blood:	n/a	n/a
32	RELA	chr21:44781528-44782587	GM18951	blood:	n/a	n/a
33	E2F6	chr21:44781871-44782669	H1-hESC	embryonic stem cell:	n/a	chr21:44782296-44782305 chr21:44782354-44782363

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr21:44781958-44782008	BE2_C	brain:	n/a
2	chr21:44781958-44782008	HAEpiC	amniotic membrane:	n/a
3	chr21:44781958-44782008	Jurkat	blood:	n/a
4	chr21:44781958-44782008	GM19239	blood:	n/a
5	chr21:44781958-44782008	HCM	heart:	n/a
6	chr21:44781958-44782008	NHBE	bronchial:	n/a
7	chr21:44781958-44782008	Caco-2	colon:	n/a
8	chr21:44781958-44782008	AG04450	lung:	fetal
9	chr21:44781958-44782008	IMR90	lung:	fetal
10	chr21:44781958-44782008	SAEC	small airway:	n/a
11	chr21:44781958-44782008	T-47D	breast:	n/a
12	chr21:44781958-44782008	ProgFib	skin:	n/a
13	chr21:44781958-44782008	PrEC	prostate:	n/a
14	chr21:44781958-44782008	H1-hESC	embryonic stem cell:	embryo
15	chr21:44781958-44782008	K562	blood:	n/a
16	chr21:44781958-44782008	Hepatocyte	liver:	n/a
17	chr21:44781958-44782008	HCF	heart:	n/a
18	chr21:44781958-44782008	HEK293	kidney:	embryo
19	chr21:44781958-44782008	AG10803	skin:	n/a
20	chr21:44781958-44782008	NH-A	brain:	n/a
21	chr21:44781958-44782008	GM12878	blood:	n/a
22	chr21:44781958-44782008	NHDF-neo	bronchial:	n/a
23	chr21:44781958-44782008	HCT-116	colon:	n/a
24	chr21:44781958-44782008	HRPEpiC	eye:	n/a
25	chr21:44781958-44782008	HPAEpiC	pulmonary alveolar:	n/a
26	chr21:44781958-44782008	HepG2	liver:	n/a
27	chr21:44781958-44782008	SK-N-SH	brain:	n/a
28	chr21:44781958-44782008	HIPEpiC	eye:	n/a
29	chr21:44781958-44782008	SKMC	muscle:	n/a
30	chr21:44781958-44782008	SK-N-SH_RA	brain:	n/a
31	chr21:44781958-44782008	HRCEpiC	kidney:	n/a
32	chr21:44781958-44782008	CMK	blood:	n/a
33	chr21:44781958-44782008	GM12891	blood:	n/a
34	chr21:44781958-44782008	ECC-1	luminal epithelium:	n/a
35	chr21:44781958-44782008	A549	lung:	n/a
36	chr21:44781958-44782008	HUVEC	blood vessel:	n/a
37	chr21:44781958-44782008	HRE	kidney:	n/a
38	chr21:44781958-44782008	NB4	blood:	n/a
39	chr21:44781958-44782008	HCPEpiC	choroid plexus:	n/a
40	chr21:44781958-44782008	LNCaP	prostate:	n/a
41	chr21:44781958-44782008	AG04449	skin:	fetal
42	chr21:44781958-44782008	HEEpiC	esophagus:	n/a
43	chr21:44781958-44782008	U87	brain:	n/a
44	chr21:44781958-44782008	GM12892	blood:	n/a
45	chr21:44781958-44782008	Hela-S3	cervix:	n/a
46	chr21:44781958-44782008	ovcar-3	ovarian:	n/a
47	chr21:44781958-44782008	HNPCEpiC	eye:	n/a
48	chr21:44781958-44782008	HL-60	blood:	n/a
49	chr21:44781958-44782008	PANC-1	pancreas:	n/a
50	chr21:44781958-44782008	HMEC	breast:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:44779798..44782094-chr21:44814719..44816894,2	MCF-7	breast:
2	chr21:44781136..44783679-chr21:44846485..44848438,3	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SIK1-5	chr21:44781863-44782209	XLOC_014102
2	lnc-SIK1-5	chr21:44781365-44782327	XLOC_014102

No data

Variant related genes	Relation type
ENSG00000225637	TF binding region
ENSG00000225637	CpG island
ENSG00000142178	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs496300	0.96[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs554253	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs559652	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs564779	1.00[YRI][hapmap]
rs565629	1.00[YRI][hapmap]
rs579870	0.92[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs634978	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs672948	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056684	chr21:44539714-44886119	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv913831	chr21:44563995-44931821	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
3	esv1817359	chr21:44699077-44821595	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1057726	chr21:44711850-44957303	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv544466	chr21:44711850-44957303	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
6	nsv1058308	chr21:44722915-44825108	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1063186	chr21:44729904-44828476	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv544467	chr21:44729904-44828476	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv913837	chr21:44731138-44853859	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv913838	chr21:44740134-44931821	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
11	nsv913839	chr21:44750200-44931821	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
12	nsv913840	chr21:44750643-44823479	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
13	nsv913841	chr21:44761874-44853859	Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
14	nsv913842	chr21:44764895-44792929	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv913843	chr21:44774757-44810756	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv913844	chr21:44779680-44875495	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS 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	82 gene(s)	inside rSNPs	diseases
17	nsv913845	chr21:44781356-44874702	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
18	nsv470901	chr21:44781356-44884252	Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44774800-44782000	Weak transcription	Brain Anterior Caudate	brain
2	chr21:44777200-44782000	Enhancers	Brain Germinal Matrix	brain
3	chr21:44777400-44788600	Enhancers	Fetal Brain Male	brain
4	chr21:44779400-44782200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr21:44780000-44783600	Enhancers	Primary B cells from cord blood	blood
6	chr21:44780200-44782000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
7	chr21:44780200-44782600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr21:44780200-44788400	Enhancers	Spleen	Spleen
9	chr21:44780400-44782000	Enhancers	Esophagus	oesophagus
10	chr21:44780600-44782000	Enhancers	Fetal Lung	lung
11	chr21:44780600-44782800	Enhancers	Fetal Heart	heart
12	chr21:44780800-44782000	Enhancers	Duodenum Mucosa	Duodenum
13	chr21:44780800-44782200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr21:44780800-44782200	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr21:44780800-44782400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr21:44780800-44782600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr21:44780800-44783000	Bivalent Enhancer	Fetal Stomach	stomach
18	chr21:44780800-44783200	Flanking Active TSS	Dnd41	blood
19	chr21:44780800-44784800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr21:44781000-44782000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr21:44781000-44782200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr21:44781000-44782200	Enhancers	Fetal Brain Female	brain
23	chr21:44781000-44782200	Enhancers	Fetal Intestine Small	intestine
24	chr21:44781000-44782600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr21:44781000-44782600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr21:44781000-44782800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr21:44781000-44782800	Flanking Active TSS	GM12878-XiMat	blood
28	chr21:44781000-44783000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr21:44781000-44784800	Weak transcription	Gastric	stomach
30	chr21:44781200-44782000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr21:44781200-44782000	Weak transcription	Brain Angular Gyrus	brain
32	chr21:44781200-44782000	Enhancers	Brain Cingulate Gyrus	brain
33	chr21:44781200-44782200	Enhancers	Brain Substantia Nigra	brain
34	chr21:44781200-44782600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr21:44781200-44782600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr21:44781200-44782600	Enhancers	Fetal Intestine Large	intestine
37	chr21:44781200-44782600	Flanking Active TSS	Fetal Muscle Leg	muscle
38	chr21:44781200-44782600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr21:44781200-44782600	Flanking Active TSS	HMEC	breast
40	chr21:44781200-44782600	Flanking Active TSS	NHEK	skin
41	chr21:44781200-44782800	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr21:44781200-44782800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
43	chr21:44781200-44782800	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr21:44781200-44782800	Enhancers	Brain Hippocampus Middle	brain
45	chr21:44781200-44782800	Enhancers	NH-A	brain
46	chr21:44781200-44783800	Enhancers	Primary hematopoietic stem cells	blood
47	chr21:44781200-44784000	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr21:44781400-44782000	Active TSS	Right Atrium	heart
49	chr21:44781400-44782200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr21:44781400-44782200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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