Variant report

Variant	rs28538864
Chromosome Location	chr15:50748848-50748849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:50748832-50749029	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:50747304..50750243-chr15:50771020..50773761,2	K562	blood:
2	chr15:50647024..50648996-chr15:50748059..50750283,2	MCF-7	breast:
3	chr15:50646803..50649457-chr15:50748073..50750428,2	MCF-7	breast:

Variant related genes	Relation type
USP8	TF binding region
ENSG00000104064	Chromatin interaction
ENSG00000244879	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs28718131	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3098166	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3098170	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3098175	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3131569	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3131570	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv948579	chr15:50645530-51045564	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv524613	chr15:50656449-50868779	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv904210	chr15:50702058-50786024	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1040717	chr15:50715572-50846521	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv1053966	chr15:50715572-51133186	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
7	nsv542383	chr15:50715572-51133186	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
8	nsv1043805	chr15:50715572-51208891	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
9	nsv542384	chr15:50715572-51208891	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
10	nsv1049576	chr15:50744781-50843495	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
12	nsv1051990	chr15:50745814-51133186	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50717600-50764600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:50717600-50774800	Weak transcription	Stomach Mucosa	stomach
3	chr15:50717800-50758800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:50718000-50755400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:50718000-50757000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:50722800-50764600	Weak transcription	Esophagus	oesophagus
7	chr15:50724600-50755800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr15:50724800-50764600	Weak transcription	Pancreas	Pancrea
9	chr15:50728200-50750200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr15:50730800-50754200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr15:50732200-50749000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:50733400-50785200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:50733600-50758200	Weak transcription	HMEC	breast
14	chr15:50733600-50758800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr15:50733800-50752800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:50733800-50755800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr15:50734000-50763200	Weak transcription	Brain Anterior Caudate	brain
18	chr15:50734000-50776400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:50734000-50785600	Weak transcription	Fetal Brain Male	brain
20	chr15:50734600-50752800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr15:50734600-50772600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr15:50735400-50764600	Weak transcription	Psoas Muscle	Psoas
23	chr15:50735600-50773000	Weak transcription	Brain Substantia Nigra	brain
24	chr15:50736200-50758600	Weak transcription	Right Ventricle	heart
25	chr15:50737200-50752600	Weak transcription	Lung	lung
26	chr15:50737200-50764800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr15:50737400-50755600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr15:50737400-50756800	Weak transcription	NHEK	skin
29	chr15:50737600-50751200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:50738200-50796800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:50738400-50755800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:50739000-50749800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr15:50739200-50750800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr15:50739400-50755200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:50740200-50777200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr15:50740800-50770200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr15:50741000-50749000	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr15:50741200-50749600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:50741800-50749400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:50741800-50750400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr15:50741800-50797000	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr15:50742400-50749000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr15:50742400-50760000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr15:50742600-50753600	Strong transcription	Primary T cells from cord blood	blood
45	chr15:50742600-50760000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:50744000-50750800	Weak transcription	NH-A	brain
47	chr15:50744000-50782400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr15:50744000-50789000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr15:50744200-50750200	Weak transcription	HSMM	muscle
50	chr15:50744200-50754200	Weak transcription	NHDF-Ad	bronchial

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