Variant report

Variant	rs2554313
Chromosome Location	chr15:52274863-52274864
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:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 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	chr15:52274592..52276702-chr15:52310865..52313254,2	MCF-7	breast:
10	chr15:52273618..52277217-chr15:52282042..52285418,5	MCF-7	breast:
11	chr15:52273987..52275289-chr15:52370394..52371967,22	MCF-7	breast:
12	chr15:52273761..52275142-chr15:52431751..52433231,16	MCF-7	breast:
13	chr15:52272930..52275289-chr15:52472014..52473869,2	MCF-7	breast:
14	chr15:52273740..52275990-chr15:52310375..52312571,2	K562	blood:
15	chr15:52274218..52275165-chr15:52370716..52372312,7	MCF-7	breast:
16	chr15:52274413..52275086-chr15:52368881..52369577,2	MCF-7	breast:
17	chr15:52273281..52276233-chr15:52432324..52433834,2	MCF-7	breast:
18	chr15:52272756..52275955-chr15:52369833..52372310,3	MCF-7	breast:
19	chr15:52274113..52275112-chr15:52370804..52371366,6	K562	blood:
20	chr15:52274621..52276183-chr15:52281079..52282709,2	MCF-7	breast:
21	chr15:52272035..52276768-chr15:52309954..52313442,7	MCF-7	breast:

No data

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

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs16964657	0.83[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs2246726	0.83[AMR][1000 genomes]
rs2414120	0.83[AMR][1000 genomes]
rs2414121	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2441779	0.83[AMR][1000 genomes]
rs2470593	0.83[AMR][1000 genomes]
rs2470594	0.83[AMR][1000 genomes]
rs2554338	0.81[AMR][1000 genomes]
rs2593189	1.00[EUR][1000 genomes]
rs3099571	0.83[AMR][1000 genomes]
rs59391908	0.82[ASN][1000 genomes]
rs8040728	0.81[AMR][1000 genomes]
rs8041281	0.83[AMR][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:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52273200-52275400	Flanking Active TSS	Dnd41	blood
2	chr15:52273800-52275000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr15:52273800-52275200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:52274600-52275000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:52274600-52275000	Enhancers	Duodenum Mucosa	Duodenum
6	chr15:52274600-52275000	Enhancers	HepG2	liver
7	chr15:52274600-52275000	Enhancers	HMEC	breast
8	chr15:52274600-52275000	Enhancers	Osteobl	bone
9	chr15:52274600-52275200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr15:52274600-52275200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:52274600-52275200	Enhancers	NHLF	lung
12	chr15:52274600-52275400	Enhancers	NHEK	skin
13	chr15:52274600-52275600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:52274600-52275600	Enhancers	HUVEC	blood vessel
15	chr15:52274600-52275800	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr15:52274600-52275800	Enhancers	Hela-S3	cervix
17	chr15:52274600-52276400	Weak transcription	Placenta	Placenta
18	chr15:52274600-52277200	Weak transcription	Fetal Intestine Small	intestine
19	chr15:52274600-52279200	Weak transcription	Right Atrium	heart
20	chr15:52274600-52284600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:52274800-52275000	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr15:52274800-52275000	Enhancers	GM12878-XiMat	blood
23	chr15:52274800-52275200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:52274800-52275200	Enhancers	Primary hematopoietic stem cells	blood
25	chr15:52274800-52275200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:52274800-52275200	Enhancers	NHDF-Ad	bronchial
27	chr15:52274800-52275400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:52274800-52275400	Enhancers	Muscle Satellite Cultured Cells	--
29	chr15:52274800-52275400	Enhancers	A549	lung
30	chr15:52274800-52275600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:52274800-52275600	Weak transcription	Stomach Mucosa	stomach
32	chr15:52274800-52278800	Weak transcription	Brain Angular Gyrus	brain
33	chr15:52274800-52287200	Weak transcription	HSMMtube	muscle

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