Variant report

Variant	rs28733269
Chromosome Location	chr17:15386298-15386299
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:15371816..15373680-chr17:15385031..15387890,2	MCF-7	breast:
2	chr17:15378837..15380721-chr17:15383271..15386899,3	K562	blood:

Variant related genes	Relation type
ENSG00000239704	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11651787	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11653403	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1465251	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1465252	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2052022	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28411195	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3865257	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4572441	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55749051	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62069953	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072569	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62072571	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62072578	0.83[EUR][1000 genomes]
rs716389	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7211982	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8076852	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9899922	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9901383	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9903674	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9908651	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9911005	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9911822	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9913509	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv949172	chr17:15206970-15416808	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1055677	chr17:15294011-15561130	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv1058286	chr17:15315763-15561130	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv543213	chr17:15315763-15561130	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15340600-15399600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr17:15359200-15404600	Weak transcription	Primary T cells from cord blood	blood
3	chr17:15359400-15386600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr17:15361200-15387800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr17:15367400-15394200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr17:15368000-15393600	Weak transcription	Aorta	Aorta
7	chr17:15368200-15386800	Weak transcription	Ovary	ovary
8	chr17:15368400-15405400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr17:15368800-15394000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr17:15369000-15393600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr17:15369000-15401600	Weak transcription	Brain Germinal Matrix	brain
12	chr17:15369200-15405000	Weak transcription	Esophagus	oesophagus
13	chr17:15369600-15386800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr17:15373200-15393600	Weak transcription	Brain Hippocampus Middle	brain
15	chr17:15373200-15393600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr17:15374600-15386800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr17:15376200-15387800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr17:15376200-15387800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr17:15376200-15387800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr17:15376200-15388000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr17:15376200-15388000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr17:15376400-15388000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr17:15377200-15394200	Weak transcription	Stomach Mucosa	stomach
24	chr17:15377400-15406400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr17:15377600-15386600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr17:15377600-15393800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr17:15378800-15391200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr17:15379200-15386600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr17:15379400-15387800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr17:15379400-15393600	Weak transcription	HSMMtube	muscle
31	chr17:15379400-15393600	Weak transcription	Osteobl	bone
32	chr17:15379600-15393800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr17:15380200-15393400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr17:15382000-15387800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr17:15382800-15386600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr17:15382800-15394400	Weak transcription	Spleen	Spleen
37	chr17:15383200-15419600	Weak transcription	Thymus	Thymus
38	chr17:15383400-15386600	Weak transcription	Small Intestine	intestine
39	chr17:15383400-15387600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr17:15383400-15390800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr17:15383400-15391000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr17:15383400-15393400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr17:15383400-15393400	Weak transcription	Right Ventricle	heart
44	chr17:15383400-15394000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr17:15383400-15402200	Weak transcription	A549	lung
46	chr17:15383400-15455000	Weak transcription	Gastric	stomach
47	chr17:15383600-15386600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr17:15383600-15386600	Weak transcription	Brain Angular Gyrus	brain
49	chr17:15383600-15386600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr17:15383600-15386600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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