Variant report

Variant	rs11089020
Chromosome Location	chr21:44939991-44939992
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:44298672..44300834-chr21:44939820..44941690,2	MCF-7	breast:
2	chr21:44584155..44585737-chr21:44938790..44941419,2	MCF-7	breast:
3	chr21:44938458..44941358-chr21:44949820..44951384,2	MCF-7	breast:
4	chr21:44935195..44942837-chr21:45027341..45034401,13	MCF-7	breast:
5	chr21:44844533..44847872-chr21:44929082..44940063,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142178	Chromatin interaction
ENSG00000160194	Chromatin interaction
ENSG00000160193	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11701518	0.84[ASN][1000 genomes]
rs11701746	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1436291	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1595167	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs162343	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs162344	0.91[AMR][1000 genomes]
rs162345	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs162367	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs162368	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs162373	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs162388	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs162389	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs162395	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs162396	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs162398	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs167930	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1836854	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1836855	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1836856	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs230640	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs230644	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs230645	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs230646	0.84[EUR][1000 genomes]
rs2876854	0.84[ASN][1000 genomes]
rs4819212	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4819219	0.84[ASN][1000 genomes]
rs56369437	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6417729	0.89[ASN][1000 genomes]
rs6518268	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7278003	0.89[ASN][1000 genomes]
rs7278282	0.84[ASN][1000 genomes]
rs7282704	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7283362	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8131020	0.84[ASN][1000 genomes]
rs9977258	0.89[ASN][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:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44928800-44941000	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr21:44929200-44943400	Enhancers	Placenta Amnion	Placenta Amnion
3	chr21:44929600-44943400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr21:44929800-44943600	Enhancers	HMEC	breast
5	chr21:44934400-44941200	Enhancers	HUVEC	blood vessel
6	chr21:44934600-44940200	Enhancers	Placenta	Placenta
7	chr21:44935400-44943400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr21:44937000-44941000	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr21:44937200-44941800	Weak transcription	Spleen	Spleen
10	chr21:44937400-44942200	Enhancers	HepG2	liver
11	chr21:44937400-44946000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr21:44937600-44943000	Enhancers	A549	lung
13	chr21:44937600-44943600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr21:44938000-44940000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr21:44938000-44940000	Weak transcription	Fetal Stomach	stomach
16	chr21:44938000-44940200	Weak transcription	Fetal Muscle Leg	muscle
17	chr21:44938200-44940000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr21:44938200-44940000	Weak transcription	Right Atrium	heart
19	chr21:44938200-44940000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr21:44938200-44940000	Weak transcription	HSMM	muscle
21	chr21:44938200-44940000	Weak transcription	NH-A	brain
22	chr21:44938400-44940000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr21:44938400-44940000	Weak transcription	Psoas Muscle	Psoas
24	chr21:44938400-44940000	Weak transcription	Stomach Mucosa	stomach
25	chr21:44938400-44941200	Enhancers	Hela-S3	cervix
26	chr21:44938400-44941600	Weak transcription	Lung	lung
27	chr21:44938400-44941600	Weak transcription	Right Ventricle	heart
28	chr21:44938400-44941600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr21:44938600-44942400	Weak transcription	Esophagus	oesophagus
30	chr21:44938600-44943400	Enhancers	NHEK	skin
31	chr21:44938600-44945400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr21:44938600-44946000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr21:44938800-44940000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr21:44939000-44940000	Weak transcription	HSMMtube	muscle
35	chr21:44939000-44942000	Weak transcription	Fetal Intestine Small	intestine
36	chr21:44939200-44943400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr21:44939600-44940400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr21:44939600-44941200	Enhancers	Muscle Satellite Cultured Cells	--
39	chr21:44939800-44940000	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr21:44939800-44940000	Enhancers	Duodenum Mucosa	Duodenum
41	chr21:44939800-44940000	Enhancers	Ovary	ovary
42	chr21:44939800-44940000	Enhancers	Small Intestine	intestine
43	chr21:44939800-44940400	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr21:44939800-44940400	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr21:44939800-44940400	Enhancers	Fetal Lung	lung
46	chr21:44939800-44940400	Enhancers	Gastric	stomach
47	chr21:44939800-44940800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr21:44939800-44941000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr21:44939800-44941000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr21:44939800-44941000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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