Variant report

Variant	rs16964657
Chromosome Location	chr15:52274413-52274414
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:26)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52273697..52275326-chr15:52431024..52433889,2	MCF-7	breast:
2	chr15:52272584..52276027-chr15:52308541..52312916,5	K562	blood:
3	chr15:52273041..52275862-chr15:52300749..52303075,2	MCF-7	breast:
4	chr15:52273823..52274921-chr15:52431326..52432805,7	MCF-7	breast:
5	chr15:52272788..52276993-chr15:52369760..52371998,4	MCF-7	breast:
6	chr15:52274239..52275037-chr15:52500239..52501186,3	MCF-7	breast:
7	chr15:52274080..52275150-chr15:52431476..52433034,10	K562	blood:
8	chr15:52273590..52276860-chr15:52313793..52315606,3	MCF-7	breast:
9	chr15:52273097..52274841-chr15:52286884..52288398,2	K562	blood:
10	chr15:52267594..52270331-chr15:52272576..52274636,3	MCF-7	breast:
11	chr15:52272443..52274627-chr15:52305698..52308304,2	K562	blood:
12	chr15:52274293..52274815-chr15:52372080..52373063,2	MCF-7	breast:
13	chr15:52273618..52277217-chr15:52282042..52285418,5	MCF-7	breast:
14	chr15:52273987..52275289-chr15:52370394..52371967,22	MCF-7	breast:
15	chr15:52274179..52274726-chr15:52310991..52311929,2	MCF-7	breast:
16	chr15:52273761..52275142-chr15:52431751..52433231,16	MCF-7	breast:
17	chr15:52272930..52275289-chr15:52472014..52473869,2	MCF-7	breast:
18	chr15:52273740..52275990-chr15:52310375..52312571,2	K562	blood:
19	chr15:52274218..52275165-chr15:52370716..52372312,7	MCF-7	breast:
20	chr15:52271865..52274806-chr15:52313995..52316353,2	MCF-7	breast:
21	chr15:52274413..52275086-chr15:52368881..52369577,2	MCF-7	breast:
22	chr15:52273281..52276233-chr15:52432324..52433834,2	MCF-7	breast:
23	chr15:52272756..52275955-chr15:52369833..52372310,3	MCF-7	breast:
24	chr15:52269337..52272220-chr15:52273087..52274635,2	MCF-7	breast:
25	chr15:52274113..52275112-chr15:52370804..52371366,6	K562	blood:
26	chr15:52272035..52276768-chr15:52309954..52313442,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259438	Chromatin interaction
ENSG00000069956	Chromatin interaction
ENSG00000069966	Chromatin interaction
ENSG00000259577	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2250797	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2414121	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2433219	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2554313	0.83[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs2554317	1.00[EUR][1000 genomes]
rs2554321	1.00[EUR][1000 genomes]
rs2554338	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2554341	1.00[EUR][1000 genomes]
rs2570246	1.00[EUR][1000 genomes]
rs2570262	1.00[EUR][1000 genomes]
rs2593196	0.81[AMR][1000 genomes]
rs2623293	1.00[EUR][1000 genomes]
rs35487339	0.81[AMR][1000 genomes]
rs59391908	0.99[ASN][1000 genomes]
rs59782457	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830255	chr15:52133914-52274863	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers 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
2	nsv1053788	chr15:52223389-52307138	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1047260	chr15:52257100-52337418	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	nsv1050664	chr15:52265723-52342101	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv517399	chr15:52266878-52305464	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv569421	chr15:52268144-52282436	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52273000-52274600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:52273200-52274600	Enhancers	Fetal Intestine Small	intestine
3	chr15:52273200-52275400	Flanking Active TSS	Dnd41	blood
4	chr15:52273400-52274600	Enhancers	Psoas Muscle	Psoas
5	chr15:52273400-52274600	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr15:52273600-52274600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr15:52273600-52274600	Flanking Active TSS	Hela-S3	cervix
8	chr15:52273600-52274800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:52273600-52274800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:52273600-52274800	Enhancers	Stomach Mucosa	stomach
11	chr15:52273800-52274600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:52273800-52274600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:52273800-52274600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:52273800-52274600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr15:52273800-52274600	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr15:52273800-52274600	Enhancers	Primary B cells from peripheral blood	blood
17	chr15:52273800-52274600	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr15:52273800-52274600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr15:52273800-52274600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr15:52273800-52274600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr15:52273800-52274600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:52273800-52274600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:52273800-52274600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:52273800-52274600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:52273800-52274600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:52273800-52274600	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr15:52273800-52274600	Flanking Active TSS	Liver	Liver
28	chr15:52273800-52274600	Flanking Active TSS	Brain Anterior Caudate	brain
29	chr15:52273800-52274600	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr15:52273800-52274600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr15:52273800-52274600	Flanking Active TSS	Colon Smooth Muscle	Colon
32	chr15:52273800-52274600	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr15:52273800-52274600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr15:52273800-52274600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr15:52273800-52274600	Enhancers	Fetal Lung	lung
36	chr15:52273800-52274600	Enhancers	Fetal Muscle Leg	muscle
37	chr15:52273800-52274600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr15:52273800-52274600	Active TSS	Stomach Smooth Muscle	stomach
39	chr15:52273800-52274600	Flanking Active TSS	HepG2	liver
40	chr15:52273800-52274600	Flanking Active TSS	HUVEC	blood vessel
41	chr15:52273800-52274600	Flanking Active TSS	NHEK	skin
42	chr15:52273800-52274600	Flanking Active TSS	Osteobl	bone
43	chr15:52273800-52274800	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr15:52273800-52274800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr15:52273800-52274800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr15:52273800-52274800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr15:52273800-52274800	Enhancers	Brain Cingulate Gyrus	brain
48	chr15:52273800-52274800	Enhancers	Placenta Amnion	Placenta Amnion
49	chr15:52273800-52274800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr15:52273800-52274800	Flanking Active TSS	A549	lung

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