Variant report

Variant	rs55678152
Chromosome Location	chr15:52465484-52465485
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52464249..52467192-chr15:52469129..52471507,3	K562	blood:
2	chr15:52462679..52469948-chr15:52470344..52473249,9	MCF-7	breast:
3	chr15:52465292..52467167-chr15:52468410..52470293,2	MCF-7	breast:
4	chr15:52447415..52450073-chr15:52464203..52465781,2	MCF-7	breast:
5	chr15:52388135..52390483-chr15:52464352..52466647,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259577	Chromatin interaction
ENSG00000069966	Chromatin interaction

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

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

rs_ID	r²[population]
rs10083575	0.89[AFR][1000 genomes]
rs10220835	1.00[AMR][1000 genomes]
rs56254654	1.00[AMR][1000 genomes]
rs56709149	1.00[AMR][1000 genomes]
rs56783306	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59415316	1.00[AMR][1000 genomes]
rs59694167	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59987655	1.00[AMR][1000 genomes]
rs60525483	1.00[AMR][1000 genomes]
rs74015611	1.00[AMR][1000 genomes]
rs74015613	1.00[AMR][1000 genomes]
rs74015616	1.00[AMR][1000 genomes]
rs74015617	0.95[AFR][1000 genomes]
rs74015620	0.89[AFR][1000 genomes]
rs74015623	0.87[AFR][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	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1047647	chr15:52425879-52469181	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52429800-52470200	Weak transcription	Fetal Brain Male	brain
2	chr15:52442200-52470400	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:52442200-52471000	Weak transcription	Brain Substantia Nigra	brain
4	chr15:52442200-52471000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:52442600-52470000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:52442600-52470400	Weak transcription	HMEC	breast
7	chr15:52443000-52470800	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:52445600-52471000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:52447400-52471000	Weak transcription	Right Atrium	heart
10	chr15:52454200-52468200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:52455600-52470800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:52455800-52467800	Weak transcription	Thymus	Thymus
13	chr15:52455800-52468400	Weak transcription	Hela-S3	cervix
14	chr15:52455800-52471000	Weak transcription	Aorta	Aorta
15	chr15:52455800-52471000	Weak transcription	Gastric	stomach
16	chr15:52456000-52468400	Weak transcription	Ovary	ovary
17	chr15:52456000-52470000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr15:52456000-52470600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:52456000-52470600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:52456000-52471000	Weak transcription	HSMMtube	muscle
21	chr15:52456200-52467200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr15:52456200-52468200	Weak transcription	Fetal Brain Female	brain
23	chr15:52456200-52468400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr15:52456200-52470200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr15:52456200-52470800	Weak transcription	Fetal Stomach	stomach
26	chr15:52456200-52470800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr15:52456200-52471000	Weak transcription	Spleen	Spleen
28	chr15:52463200-52470600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr15:52463600-52468400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:52463600-52470400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:52463800-52466600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr15:52463800-52470600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:52464000-52469600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr15:52464000-52470000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr15:52464000-52470200	Weak transcription	NHEK	skin
36	chr15:52464000-52470800	Weak transcription	HUVEC	blood vessel
37	chr15:52464000-52471000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr15:52464200-52468000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr15:52464200-52468400	Weak transcription	Primary B cells from cord blood	blood
40	chr15:52464200-52468400	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr15:52464200-52468800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr15:52464200-52469800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:52464200-52470200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr15:52464200-52470400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:52464400-52465800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr15:52464400-52468400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:52464400-52468400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr15:52464400-52468400	Weak transcription	Brain Angular Gyrus	brain
49	chr15:52464400-52468600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:52464400-52470000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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