Variant report

Variant	rs17004589
Chromosome Location	chr21:45030036-45030037
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45028297..45030345-chr21:45061837..45063899,2	MCF-7	breast:
2	chr21:45024840..45027309-chr21:45029580..45031203,2	MCF-7	breast:
3	chr21:45018445..45020726-chr21:45029673..45031600,2	MCF-7	breast:
4	chr21:45014001..45016149-chr21:45027963..45031277,3	MCF-7	breast:
5	chr21:45005141..45010452-chr21:45028185..45033118,8	MCF-7	breast:
6	chr21:45021063..45023504-chr21:45029932..45031964,2	MCF-7	breast:
7	chr21:44907751..44909575-chr21:45027972..45030123,2	MCF-7	breast:
8	chr21:44997574..45001313-chr21:45028086..45031280,4	MCF-7	breast:
9	chr21:44935195..44942837-chr21:45027341..45034401,13	MCF-7	breast:
10	chr21:44923063..44923876-chr21:45029401..45030153,2	MCF-7	breast:
11	chr21:44844034..44848270-chr21:45029628..45031789,3	MCF-7	breast:
12	chr21:44595703..44598660-chr21:45028207..45031192,2	MCF-7	breast:
13	chr21:45029356..45032047-chr21:45057699..45061512,4	MCF-7	breast:
14	chr21:44847194..44850306-chr21:45028262..45031203,4	MCF-7	breast:
15	chr21:44940137..44942720-chr21:45027959..45031843,3	MCF-7	breast:
16	chr21:44920414..44926751-chr21:45027970..45034874,9	MCF-7	breast:
17	chr21:45019163..45020714-chr21:45029148..45031854,2	K562	blood:
18	chr21:44933239..44939119-chr21:45027942..45032046,11	MCF-7	breast:
19	chr21:45029800..45031671-chr21:45038220..45041944,3	MCF-7	breast:
20	chr21:45029752..45032331-chr21:45036634..45039497,2	MCF-7	breast:
21	chr21:45009238..45012189-chr21:45029511..45032580,3	MCF-7	breast:
22	chr21:44919342..44924591-chr21:45027154..45033706,9	MCF-7	breast:
23	chr21:44930776..44932782-chr21:45029722..45031947,2	MCF-7	breast:
24	chr1:204379769..204381859-chr21:45028455..45030497,2	MCF-7	breast:
25	chr21:44926667..44929719-chr21:45029857..45032741,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000158615	Chromatin interaction
ENSG00000142178	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10427514	0.92[YRI][hapmap];0.83[AMR][1000 genomes]
rs10483077	0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10483078	0.92[YRI][hapmap];0.83[AMR][1000 genomes]
rs11089065	0.92[AMR][1000 genomes]
rs11089090	0.91[YRI][hapmap]
rs11908893	0.82[AFR][1000 genomes]
rs11908919	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11909195	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11909530	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11909813	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11909916	0.83[AMR][1000 genomes]
rs11909999	0.92[AMR][1000 genomes]
rs11910220	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11910351	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11910352	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11911293	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs11911483	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11911735	0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11911856	0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12106371	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12106423	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12106466	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs13339951	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17004507	0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004580	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17004581	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004582	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17004585	0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004586	0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004587	0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004588	0.82[AFR][1000 genomes]
rs17004590	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004592	0.92[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004593	0.92[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004594	0.92[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004595	0.92[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004596	0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004600	0.80[YRI][hapmap]
rs17004602	0.80[YRI][hapmap]
rs28431406	0.83[AMR][1000 genomes]
rs28782771	0.83[AMR][1000 genomes]
rs28852206	0.83[AMR][1000 genomes]
rs59298188	0.85[AMR][1000 genomes]
rs9917493	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913873	chr21:44879869-45142427	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv1061539	chr21:44915533-45041824	Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1067171	chr21:44921187-45039471	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv521700	chr21:44925334-45041790	Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
5	nsv470903	chr21:44925334-45061501	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
6	nsv459289	chr21:44925334-45064600	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
7	nsv587690	chr21:44925334-45064600	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
8	nsv834106	chr21:44992387-45109489	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	15 gene(s)	inside rSNPs	diseases
9	nsv587700	chr21:45007956-45095200	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45021200-45030600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr21:45024400-45030600	Enhancers	NHEK	skin
3	chr21:45025600-45030400	Enhancers	Muscle Satellite Cultured Cells	--
4	chr21:45026200-45032200	Enhancers	HMEC	breast
5	chr21:45026800-45031200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr21:45027400-45030600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr21:45027600-45030800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr21:45027800-45030200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr21:45027800-45030200	Enhancers	Osteobl	bone
10	chr21:45028000-45030200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr21:45028600-45031800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr21:45028600-45032800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr21:45028800-45030200	Enhancers	Adipose Nuclei	Adipose
14	chr21:45028800-45030800	Enhancers	Fetal Heart	heart
15	chr21:45028800-45032000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr21:45029000-45030200	Enhancers	Fetal Lung	lung
17	chr21:45029000-45030600	Enhancers	Colonic Mucosa	Colon
18	chr21:45029000-45031800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr21:45029000-45033000	Enhancers	Fetal Intestine Small	intestine
20	chr21:45029200-45030200	Enhancers	HSMM	muscle
21	chr21:45029200-45030400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr21:45029200-45031800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr21:45029200-45032200	Enhancers	Fetal Intestine Large	intestine
24	chr21:45029400-45030200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr21:45029400-45030200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr21:45029400-45030200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr21:45029400-45030200	Enhancers	Liver	Liver
28	chr21:45029400-45030200	Enhancers	Brain Hippocampus Middle	brain
29	chr21:45029400-45030200	Enhancers	Brain Substantia Nigra	brain
30	chr21:45029400-45030200	Enhancers	Colon Smooth Muscle	Colon
31	chr21:45029400-45030200	Enhancers	Duodenum Mucosa	Duodenum
32	chr21:45029400-45030200	Enhancers	Esophagus	oesophagus
33	chr21:45029400-45030200	Enhancers	Fetal Stomach	stomach
34	chr21:45029400-45030200	Enhancers	Right Atrium	heart
35	chr21:45029400-45030200	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr21:45029400-45030200	Flanking Active TSS	HepG2	liver
37	chr21:45029400-45030200	Enhancers	HUVEC	blood vessel
38	chr21:45029400-45030200	Enhancers	NHLF	lung
39	chr21:45029400-45030400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr21:45029400-45030400	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr21:45029400-45030600	Enhancers	Fetal Muscle Trunk	muscle
42	chr21:45029400-45030600	Enhancers	Small Intestine	intestine
43	chr21:45029400-45030800	Enhancers	Placenta	Placenta
44	chr21:45029400-45032200	Enhancers	Placenta Amnion	Placenta Amnion
45	chr21:45029400-45032200	Enhancers	Stomach Mucosa	stomach
46	chr21:45029600-45030200	Enhancers	Brain Cingulate Gyrus	brain
47	chr21:45029600-45030200	Enhancers	Brain Germinal Matrix	brain
48	chr21:45029600-45030200	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr21:45029600-45030400	Enhancers	HSMMtube	muscle
50	chr21:45029800-45032000	Enhancers	Fetal Thymus	thymus

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