Variant report

Variant	rs17004572
Chromosome Location	chr21:44934871-44934872
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:44839515..44855046-chr21:44918803..44938582,70	MCF-7	breast:
2	chr21:44934187..44937130-chr21:45020979..45023437,3	MCF-7	breast:
3	chr21:44932624..44935080-chr21:45061728..45063349,2	K562	blood:
4	chr21:44909088..44910939-chr21:44934470..44936766,2	MCF-7	breast:
5	chr21:44763296..44765156-chr21:44933587..44936210,2	MCF-7	breast:
6	chr21:44933239..44939119-chr21:45027942..45032046,11	MCF-7	breast:
7	chr21:44849473..44851982-chr21:44934028..44935946,2	MCF-7	breast:
8	chr21:44932097..44937071-chr21:45004878..45007611,5	MCF-7	breast:
9	chr21:44934396..44939488-chr21:45063795..45068503,7	MCF-7	breast:
10	chr21:44907112..44908656-chr21:44934186..44935921,2	K562	blood:
11	chr21:44763228..44765264-chr21:44934553..44936247,2	MCF-7	breast:
12	chr21:44896300..44899568-chr21:44934496..44937957,5	MCF-7	breast:
13	chr21:44933741..44936265-chr21:45043174..45044886,2	MCF-7	breast:
14	chr21:44844533..44847872-chr21:44929082..44940063,13	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000142178	Chromatin interaction
ENSG00000185186	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11089065	0.85[YRI][hapmap]
rs11910352	0.83[YRI][hapmap]
rs11911243	1.00[EUR][1000 genomes]
rs12106371	0.85[YRI][hapmap]
rs12106423	0.85[YRI][hapmap]
rs12106466	0.85[YRI][hapmap]
rs13339951	0.85[YRI][hapmap]
rs17004570	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17004571	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17004580	0.85[YRI][hapmap]
rs17004582	0.85[YRI][hapmap]
rs17004605	0.84[EUR][1000 genomes]
rs2117981	0.92[YRI][hapmap]
rs2117983	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4819297	0.84[EUR][1000 genomes]
rs56698438	1.00[EUR][1000 genomes]
rs57734276	0.96[EUR][1000 genomes]
rs58248685	1.00[EUR][1000 genomes]
rs60365395	0.80[EUR][1000 genomes]
rs60772506	1.00[EUR][1000 genomes]
rs61060243	0.84[EUR][1000 genomes]
rs61105490	1.00[EUR][1000 genomes]
rs73906592	0.96[EUR][1000 genomes]
rs73906595	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73906600	1.00[EUR][1000 genomes]
rs73906601	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73908372	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv913868	chr21:44835508-44954522	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers 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 miRNA target site	98 gene(s)	inside rSNPs	diseases
4	esv1839560	chr21:44864079-44973184	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
5	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
6	nsv587689	chr21:44884252-44986050	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
7	nsv1059264	chr21:44895863-44944515	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	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

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44919800-44936800	Weak transcription	Fetal Brain Female	brain
2	chr21:44922800-44936000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr21:44923400-44936600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr21:44923400-44936600	Weak transcription	Brain Germinal Matrix	brain
5	chr21:44926800-44938200	Enhancers	Fetal Thymus	thymus
6	chr21:44928800-44941000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr21:44929200-44937800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr21:44929200-44938200	Enhancers	HSMM	muscle
9	chr21:44929200-44943400	Enhancers	Placenta Amnion	Placenta Amnion
10	chr21:44929600-44943400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr21:44929800-44938600	Enhancers	Esophagus	oesophagus
12	chr21:44929800-44938800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr21:44929800-44943600	Enhancers	HMEC	breast
14	chr21:44930200-44938400	Enhancers	Pancreas	Pancrea
15	chr21:44930200-44939000	Enhancers	Fetal Intestine Small	intestine
16	chr21:44930400-44935800	Enhancers	HepG2	liver
17	chr21:44930600-44939800	Enhancers	Fetal Intestine Large	intestine
18	chr21:44930800-44937800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr21:44931400-44936400	Weak transcription	Fetal Kidney	kidney
20	chr21:44931800-44935000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr21:44932000-44937200	Weak transcription	Colon Smooth Muscle	Colon
22	chr21:44932200-44936200	Weak transcription	Fetal Heart	heart
23	chr21:44932400-44936400	Enhancers	Stomach Mucosa	stomach
24	chr21:44932600-44937800	Enhancers	Liver	Liver
25	chr21:44932800-44935400	Weak transcription	Fetal Stomach	stomach
26	chr21:44932800-44935600	Genic enhancers	HSMMtube	muscle
27	chr21:44932800-44936400	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr21:44933400-44935800	Weak transcription	Fetal Lung	lung
29	chr21:44933400-44938200	Enhancers	Muscle Satellite Cultured Cells	--
30	chr21:44933600-44936000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr21:44933600-44936000	Weak transcription	Spleen	Spleen
32	chr21:44934000-44935600	Enhancers	Colonic Mucosa	Colon
33	chr21:44934000-44936000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr21:44934000-44936000	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr21:44934000-44936400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr21:44934000-44938400	Enhancers	Adipose Nuclei	Adipose
37	chr21:44934000-44938400	Enhancers	Left Ventricle	heart
38	chr21:44934000-44938400	Enhancers	Lung	lung
39	chr21:44934200-44935200	Weak transcription	Hela-S3	cervix
40	chr21:44934200-44935600	Weak transcription	Ovary	ovary
41	chr21:44934200-44935600	Genic enhancers	A549	lung
42	chr21:44934200-44935800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr21:44934200-44936200	Enhancers	NHEK	skin
44	chr21:44934200-44936800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr21:44934200-44937800	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr21:44934200-44937800	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr21:44934200-44938000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr21:44934200-44938000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr21:44934200-44938000	Enhancers	Duodenum Mucosa	Duodenum
50	chr21:44934400-44935000	Enhancers	Right Ventricle	heart

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