Variant report

Variant	rs28490099
Chromosome Location	chr21:45200252-45200253
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45137876..45142347-chr21:45194759..45200624,9	MCF-7	breast:
2	chr21:45132246..45134583-chr21:45199684..45202380,3	MCF-7	breast:
3	chr21:45137531..45139514-chr21:45200064..45202658,2	MCF-7	breast:
4	chr21:45166127..45168190-chr21:45198985..45201869,2	K562	blood:

Variant related genes	Relation type
ENSG00000160209	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs28581805	1.00[EUR][1000 genomes]
rs57815996	1.00[EUR][1000 genomes]
rs59339575	1.00[EUR][1000 genomes]
rs61299327	1.00[EUR][1000 genomes]
rs6383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73908377	1.00[EUR][1000 genomes]
rs73908383	1.00[EUR][1000 genomes]
rs8127335	1.00[EUR][1000 genomes]
rs8129408	1.00[EUR][1000 genomes]
rs8129421	1.00[EUR][1000 genomes]
rs8132097	1.00[EUR][1000 genomes]
rs8132862	1.00[EUR][1000 genomes]
rs9974076	1.00[EUR][1000 genomes]
rs9978334	1.00[EUR][1000 genomes]
rs9979923	1.00[EUR][1000 genomes]
rs9984929	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531544	chr21:45071371-45202912	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv531545	chr21:45095397-45395904	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv913876	chr21:45119629-45267193	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2830066	chr21:45133868-45258047	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv913879	chr21:45145286-45237039	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv913880	chr21:45145286-45263920	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv913881	chr21:45145286-45267193	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv1055154	chr21:45148076-45203162	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv470904	chr21:45151045-45258047	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	nsv913882	chr21:45151874-45370715	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv834107	chr21:45155325-45294546	Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
12	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
13	nsv520305	chr21:45175958-45246326	Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	nsv834108	chr21:45178037-45369641	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
15	nsv913883	chr21:45191139-45252838	Weak transcription Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
16	nsv913884	chr21:45191139-45255836	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
17	nsv544469	chr21:45194085-45257959	Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45196800-45200600	Weak transcription	NHEK	skin
2	chr21:45196800-45201000	Weak transcription	Fetal Intestine Large	intestine
3	chr21:45196800-45202000	Weak transcription	Liver	Liver
4	chr21:45196800-45203000	Weak transcription	Lung	lung
5	chr21:45196800-45206400	Weak transcription	Gastric	stomach
6	chr21:45196800-45206400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr21:45196800-45208800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr21:45196800-45209000	Weak transcription	Aorta	Aorta
9	chr21:45197000-45200800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr21:45198200-45200800	Enhancers	GM12878-XiMat	blood
11	chr21:45198800-45200800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr21:45198800-45206400	Weak transcription	Spleen	Spleen
13	chr21:45198800-45206600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr21:45199000-45200400	Weak transcription	Placenta	Placenta
15	chr21:45199000-45200600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr21:45199000-45201000	Weak transcription	Fetal Intestine Small	intestine
17	chr21:45199000-45202000	Weak transcription	Hela-S3	cervix
18	chr21:45199000-45202600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr21:45199000-45202800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr21:45199000-45202800	Weak transcription	A549	lung
21	chr21:45199000-45203000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr21:45199000-45203000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr21:45199000-45203000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr21:45199000-45206400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr21:45199000-45208600	Weak transcription	Stomach Mucosa	stomach
26	chr21:45199000-45208800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr21:45199200-45200800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr21:45199200-45202200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr21:45199200-45202400	Weak transcription	HMEC	breast
30	chr21:45199200-45202800	Enhancers	HepG2	liver
31	chr21:45199200-45204200	Weak transcription	K562	blood
32	chr21:45199200-45208400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr21:45199200-45208600	Weak transcription	Primary T cells from cord blood	blood
34	chr21:45199400-45200400	Weak transcription	Colonic Mucosa	Colon
35	chr21:45199400-45201000	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr21:45199400-45202200	Weak transcription	Adipose Nuclei	Adipose
37	chr21:45199400-45202400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr21:45199400-45202800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr21:45199400-45208600	Weak transcription	Primary B cells from cord blood	blood
40	chr21:45199800-45200600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr21:45199800-45201800	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr21:45199800-45202400	Weak transcription	Fetal Thymus	thymus
43	chr21:45200000-45200400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr21:45200000-45200400	Weak transcription	Esophagus	oesophagus
45	chr21:45200000-45203000	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr21:45200000-45206400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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