Variant report

Variant	rs17289578
Chromosome Location	chr21:46221114-46221115
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:251)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:251 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr21:46220980-46221130	HFF-Myc	foreskin:	n/a	n/a
2	MAZ	chr21:46220875-46221342	K562	blood:	n/a	n/a
3	GABPA	chr21:46221037-46222269	HL-60	blood:	n/a	chr21:46221780-46221791 chr21:46221782-46221791 chr21:46221780-46221794
4	MAX	chr21:46220947-46222556	Hela-S3	cervix:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
5	CTCF	chr21:46220956-46221314	HepG2	liver:	n/a	n/a
6	SREBP2	chr21:46220984-46222111	GM12878	blood:	n/a	n/a
7	CTCF	chr21:46221080-46221230	HMEC	breast:	n/a	n/a
8	CTCF	chr21:46221100-46221250	HCM	heart:	n/a	n/a
9	CTCF	chr21:46220991-46221351	IMR90	lung:	n/a	n/a
10	MYC	chr21:46221051-46222484	A549	lung:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
11	POLR2A	chr21:46220923-46223514	MCF10A-Er-Src	breast:	n/a	n/a
12	CTCF	chr21:46221024-46221232	LNCaP	prostate:	n/a	n/a
13	ZNF143	chr21:46220967-46221300	GM12878	blood:	n/a	n/a
14	CTCF	chr21:46220925-46221344	K562	blood:	n/a	n/a
15	GABPA	chr21:46220816-46222492	MCF-7	breast:	n/a	chr21:46221780-46221791 chr21:46221782-46221791 chr21:46221780-46221794
16	CTCF	chr21:46221080-46221230	A549	lung:	n/a	n/a
17	JUND	chr21:46220780-46221986	K562	blood:	n/a	n/a
18	CTCF	chr21:46221060-46221210	HCPEpiC	choroid plexus:	n/a	n/a
19	CTCF	chr21:46221100-46221250	GM12871	blood:	n/a	n/a
20	CTCF	chr21:46221040-46221190	GM12867	blood:	n/a	n/a
21	MAX	chr21:46220971-46222659	K562	blood:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
22	POLR2A	chr21:46220877-46225649	K562	blood:	n/a	n/a
23	CTCF	chr21:46221060-46221210	K562	blood:	n/a	n/a
24	CTCF	chr21:46221040-46221190	HPF	lung:	n/a	n/a
25	CTCF	chr21:46220886-46221441	K562	blood:	n/a	n/a
26	CTCF	chr21:46221051-46221227	Lung_OC	lung:	n/a	n/a
27	SIN3A	chr21:46220887-46222973	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr21:46221059-46221242	Hela-S3	cervix:	n/a	n/a
29	RAD21	chr21:46221009-46221280	SK-N-SH_RA	brain:	n/a	n/a
30	POLR2A	chr21:46221100-46221482	K562	blood:	n/a	n/a
31	CTCF	chr21:46221100-46221250	AG10803	skin:	n/a	n/a
32	POLR2A	chr21:46220980-46225308	K562	blood:	n/a	n/a
33	CTCF	chr21:46220909-46221498	GM12878	blood:	n/a	n/a
34	TBP	chr21:46220886-46222735	K562	blood:	n/a	n/a
35	MAX	chr21:46221015-46223263	HepG2	liver:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
36	RCOR1	chr21:46220868-46221390	K562	blood:	n/a	n/a
37	CTCF	chr21:46221000-46221150	GM12869	blood:	n/a	n/a
38	CTCF	chr21:46221060-46221210	AoAF	blood vessel:	n/a	n/a
39	CTCF	chr21:46221060-46221210	HCT-116	colon:	n/a	n/a
40	POLR2A	chr21:46220710-46226000	K562	blood:	n/a	n/a
41	GATA1	chr21:46220892-46221894	PBDE	blood:	n/a	n/a
42	CTCF	chr21:46221080-46221230	HBMEC	blood vessel:	n/a	n/a
43	MAX	chr21:46220910-46222976	MCF-7	breast:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
44	POLR2A	chr21:46220981-46225932	K562	blood:	n/a	n/a
45	CTCF	chr21:46221040-46221190	HFF	foreskin:	n/a	n/a
46	MAX	chr21:46221032-46222559	A549	lung:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
47	SIN3AK20	chr21:46221068-46221296	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr21:46221080-46221230	HMF	breast:	n/a	n/a
49	MYC	chr21:46220905-46223032	K562	blood:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
50	POLR2A	chr21:46220902-46222038	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46218606..46224662-chr21:46357422..46363606,13	MCF-7	breast:
2	chr21:46220374..46222087-chr21:46311415..46314337,2	MCF-7	breast:
3	chr21:45928985..45931297-chr21:46219796..46221889,2	MCF-7	breast:
4	chr21:46218558..46223428-chr21:46289542..46296056,15	MCF-7	breast:
5	chr21:45718752..45721154-chr21:46219831..46222611,2	K562	blood:
6	chr21:46220974..46223841-chr21:46346856..46349461,2	K562	blood:
7	chr21:46220554..46223722-chr21:46306934..46310028,3	MCF-7	breast:
8	chr21:46220974..46223825-chr21:46494380..46498218,5	MCF-7	breast:
9	chr21:46220726..46223224-chr21:46328113..46331561,4	K562	blood:
10	chr21:46219434..46222664-chr21:46346417..46349763,6	MCF-7	breast:
11	chr21:46220151..46222677-chr21:46492186..46495962,3	K562	blood:
12	chr21:46220930..46225769-chr21:46292170..46294469,5	K562	blood:
13	chr21:46218496..46222154-chr21:46279503..46283710,3	MCF-7	breast:
14	chr21:46221113..46222920-chr21:46311601..46314491,2	K562	blood:
15	chr21:46220413..46223818-chr21:46291771..46295209,8	K562	blood:
16	chr21:46220308..46222402-chr21:46328701..46333083,4	MCF-7	breast:
17	chr21:45927714..45931885-chr21:46220128..46224260,6	MCF-7	breast:
18	chr21:46220260..46222802-chr21:46358731..46365262,8	MCF-7	breast:
19	chr20:45984634..45987262-chr21:46219843..46222143,2	MCF-7	breast:
20	chr21:46217105..46224485-chr21:46287607..46297526,26	MCF-7	breast:
21	chr21:46220263..46223201-chr21:46349640..46352735,4	K562	blood:
22	chr21:46220228..46226309-chr21:46349546..46355767,8	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTTG1IP-1	chr21:46219905-46221313	NONHSAT082879

No data

Variant related genes	Relation type
ENSG00000236519	TF binding region
ENSG00000101040	Chromatin interaction
ENSG00000273027	Chromatin interaction
ENSG00000141959	Chromatin interaction
ENSG00000235374	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000160256	Chromatin interaction
ENSG00000183255	Chromatin interaction
ENSG00000268856	Chromatin interaction
ENSG00000183250	Chromatin interaction
ENSG00000160255	Chromatin interaction
ENSG00000235890	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1051331	0.80[EUR][1000 genomes]
rs1141	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17217834	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17289745	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017089	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838681	1.00[ASN][1000 genomes]
rs2838683	1.00[ASN][1000 genomes]
rs2838689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838690	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2838691	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2838692	0.80[EUR][1000 genomes]
rs28728356	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs428428	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232950	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8645	0.80[EUR][1000 genomes]
rs873301	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9977480	0.80[EUR][1000 genomes]
rs9977684	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46219600-46221400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr21:46219800-46222400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr21:46220000-46221200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr21:46220000-46221200	Flanking Active TSS	Osteobl	bone
5	chr21:46220000-46221600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr21:46220000-46222400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr21:46220200-46221200	Flanking Active TSS	Duodenum Mucosa	Duodenum
8	chr21:46220200-46221200	Flanking Active TSS	Fetal Brain Female	brain
9	chr21:46220200-46221200	Flanking Active TSS	HUVEC	blood vessel
10	chr21:46220200-46221600	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr21:46220200-46222600	Active TSS	Fetal Kidney	kidney
12	chr21:46220200-46222600	Active TSS	A549	lung
13	chr21:46220400-46221200	Flanking Active TSS	Brain Angular Gyrus	brain
14	chr21:46220400-46221200	Flanking Active TSS	Brain Anterior Caudate	brain
15	chr21:46220400-46221200	Flanking Active TSS	Brain Cingulate Gyrus	brain
16	chr21:46220400-46221200	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr21:46220400-46221200	Flanking Active TSS	Colon Smooth Muscle	Colon
18	chr21:46220400-46221200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr21:46220400-46221400	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr21:46220400-46221400	Flanking Active TSS	Liver	Liver
21	chr21:46220400-46221400	Flanking Active TSS	Rectal Smooth Muscle	rectum
22	chr21:46220400-46221600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr21:46220400-46221600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr21:46220400-46221600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr21:46220400-46221600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr21:46220400-46222000	Active TSS	Fetal Muscle Trunk	muscle
27	chr21:46220400-46222600	Active TSS	H1 Cell Line	embryonic stem cell
28	chr21:46220400-46222800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr21:46220400-46223000	Active TSS	H9 Cell Line	embryonic stem cell
30	chr21:46220600-46221200	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr21:46220600-46221200	Flanking Active TSS	Dnd41	blood
32	chr21:46220600-46221400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr21:46220600-46221400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr21:46220600-46221400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr21:46220600-46222200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr21:46220600-46222400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr21:46220600-46222400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr21:46220600-46222400	Active TSS	Fetal Intestine Large	intestine
39	chr21:46220600-46222600	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr21:46220600-46222600	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr21:46220600-46222800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr21:46220600-46222800	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr21:46220600-46222800	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr21:46220800-46221200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr21:46220800-46221200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr21:46220800-46221200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr21:46220800-46221200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr21:46220800-46221200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr21:46220800-46221400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
50	chr21:46220800-46221400	Flanking Active TSS	Primary T cells fromperipheralblood	blood

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