Variant report

Variant	rs2554346
Chromosome Location	chr15:52243284-52243285
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52241158..52244077-chr15:52263523..52265135,2	MCF-7	breast:
2	chr15:52241662..52244027-chr15:52256794..52258738,3	MCF-7	breast:
3	chr15:52242423..52244637-chr15:52246351..52249201,2	K562	blood:
4	chr15:52232725..52234796-chr15:52242027..52243795,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166477	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs11446467	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1426085	0.81[AFR][1000 genomes]
rs1824083	0.86[YRI][hapmap]
rs1867985	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2162224	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs2250797	0.84[AFR][1000 genomes]
rs2436663	0.94[YRI][hapmap];0.87[AFR][1000 genomes]
rs2436664	0.94[YRI][hapmap]
rs2470592	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470606	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470614	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554310	0.82[YRI][hapmap]
rs2554311	0.81[AFR][1000 genomes]
rs2554312	0.93[AFR][1000 genomes]
rs2554318	0.83[AFR][1000 genomes]
rs2554319	0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554320	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554321	0.87[YRI][hapmap]
rs2554323	0.81[AFR][1000 genomes]
rs2554324	0.94[YRI][hapmap];0.87[AFR][1000 genomes]
rs2554329	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs2554331	0.80[YRI][hapmap]
rs2554333	0.94[YRI][hapmap]
rs2554341	0.87[YRI][hapmap]
rs2554344	0.87[AFR][1000 genomes]
rs2554352	0.94[YRI][hapmap]
rs2554356	0.94[YRI][hapmap]
rs2554357	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2570218	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs2570220	0.81[AFR][1000 genomes]
rs2570221	0.81[AFR][1000 genomes]
rs2570222	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2570223	0.93[AFR][1000 genomes]
rs2570232	0.93[YRI][hapmap]
rs2570242	0.93[YRI][hapmap]
rs2570244	0.94[YRI][hapmap]
rs2570245	0.94[YRI][hapmap]
rs2570246	0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs2570249	0.93[YRI][hapmap]
rs2570250	0.93[YRI][hapmap]
rs2570256	0.94[YRI][hapmap]
rs2570257	0.94[YRI][hapmap]
rs2570266	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2570267	0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs2570270	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2570272	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2570273	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs2593165	0.81[AFR][1000 genomes]
rs2593171	0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2593172	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2593175	0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs2593176	0.81[AFR][1000 genomes]
rs2593178	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2593180	0.81[AFR][1000 genomes]
rs2593186	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2593197	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2593203	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2623246	0.94[YRI][hapmap]
rs2623248	0.94[YRI][hapmap]
rs2623250	0.93[YRI][hapmap]
rs2623264	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs2623269	0.94[YRI][hapmap]
rs2623273	0.87[AFR][1000 genomes]
rs2623274	0.94[YRI][hapmap];0.87[AFR][1000 genomes]
rs2623275	0.87[AFR][1000 genomes]
rs2623277	0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs2623278	0.81[AFR][1000 genomes]
rs2623287	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs2623290	0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2623293	0.88[YRI][hapmap]
rs2652596	0.86[YRI][hapmap]
rs2916174	0.81[AFR][1000 genomes]
rs2959297	0.83[AFR][1000 genomes]
rs3099570	0.83[AFR][1000 genomes]
rs543024	0.86[YRI][hapmap]
rs562858	0.86[YRI][hapmap]
rs690433	0.87[YRI][hapmap]
rs73396698	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs919056	0.81[YRI][hapmap]
rs919057	0.87[YRI][hapmap]
rs919058	0.87[AFR][1000 genomes]
rs990666	0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	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
3	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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52179600-52259800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:52200400-52262200	Weak transcription	Stomach Mucosa	stomach
3	chr15:52222600-52259800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:52223200-52245400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:52226000-52255200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:52226200-52254800	Strong transcription	Thymus	Thymus
7	chr15:52226200-52255000	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr15:52226200-52259400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:52227400-52255000	Strong transcription	Liver	Liver
10	chr15:52227400-52258400	Strong transcription	Dnd41	blood
11	chr15:52227800-52255000	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr15:52229400-52249000	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr15:52229800-52254200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:52232800-52256000	Strong transcription	Fetal Muscle Leg	muscle
15	chr15:52233000-52258000	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr15:52233200-52250800	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr15:52233200-52255200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr15:52233200-52255200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:52233400-52248000	Strong transcription	Primary T cells from cord blood	blood
20	chr15:52233600-52258000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr15:52235600-52255000	Strong transcription	Duodenum Mucosa	Duodenum
22	chr15:52235600-52255200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:52235600-52256000	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:52235600-52258000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:52235800-52255000	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr15:52235800-52255000	Strong transcription	A549	lung
27	chr15:52235800-52255000	Strong transcription	Osteobl	bone
28	chr15:52235800-52255200	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr15:52235800-52255200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:52235800-52256000	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:52235800-52258000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:52235800-52258600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr15:52235800-52259200	Strong transcription	Hela-S3	cervix
34	chr15:52236000-52248400	Strong transcription	GM12878-XiMat	blood
35	chr15:52236000-52248600	Strong transcription	HSMMtube	muscle
36	chr15:52236000-52255000	Strong transcription	Stomach Smooth Muscle	stomach
37	chr15:52236000-52255200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:52236000-52255200	Strong transcription	Fetal Lung	lung
39	chr15:52236000-52255600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr15:52236000-52256200	Strong transcription	HepG2	liver
41	chr15:52236000-52258000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:52236000-52258600	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:52236000-52258800	Strong transcription	Fetal Thymus	thymus
44	chr15:52236200-52255600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:52236200-52258800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:52236400-52246600	Strong transcription	Fetal Brain Female	brain
47	chr15:52236400-52247000	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr15:52236400-52254800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr15:52236600-52255200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:52236800-52254600	Strong transcription	Fetal Intestine Large	intestine

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