Variant report

Variant	rs2470606
Chromosome Location	chr15:52256787-52256788
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52251464..52253860-chr15:52255270..52257201,2	K562	blood:
2	chr15:52250643..52258110-chr15:52261122..52265819,12	MCF-7	breast:
3	chr15:52247928..52250434-chr15:52253574..52257568,3	MCF-7	breast:
4	chr15:52250021..52252100-chr15:52255558..52257504,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166477	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11446467	0.83[AMR][1000 genomes]
rs1867985	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2250797	0.87[AFR][1000 genomes]
rs2436663	0.84[AFR][1000 genomes]
rs2470592	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470614	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554312	0.90[AFR][1000 genomes]
rs2554318	0.86[AFR][1000 genomes]
rs2554319	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554320	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554324	0.84[AFR][1000 genomes]
rs2554329	0.84[AFR][1000 genomes]
rs2554344	0.84[AFR][1000 genomes]
rs2554346	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554357	0.88[AFR][1000 genomes]
rs2570222	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2570223	0.90[AFR][1000 genomes]
rs2570266	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2570270	0.83[AFR][1000 genomes]
rs2570272	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2593171	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2593172	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2593178	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2593186	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2593197	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2593203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2623273	0.84[AFR][1000 genomes]
rs2623274	0.84[AFR][1000 genomes]
rs2623275	0.84[AFR][1000 genomes]
rs2623290	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2959297	0.86[AFR][1000 genomes]
rs3099570	0.86[AFR][1000 genomes]
rs35487339	0.81[AFR][1000 genomes]
rs73396698	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs919058	0.84[AFR][1000 genomes]

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:125 , 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	chr15:52226200-52259400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:52227400-52258400	Strong transcription	Dnd41	blood
6	chr15:52233000-52258000	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr15:52233600-52258000	Strong transcription	Primary B cells from peripheral blood	blood
8	chr15:52235600-52258000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:52235800-52258000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:52235800-52258600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr15:52235800-52259200	Strong transcription	Hela-S3	cervix
12	chr15:52236000-52258000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:52236000-52258600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:52236000-52258800	Strong transcription	Fetal Thymus	thymus
15	chr15:52236200-52258800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:52237000-52258400	Strong transcription	Fetal Muscle Trunk	muscle
17	chr15:52237200-52257600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr15:52244400-52257400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr15:52244600-52262600	Weak transcription	Fetal Heart	heart
20	chr15:52245600-52261800	Weak transcription	Pancreas	Pancrea
21	chr15:52245600-52262600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr15:52245800-52258000	Weak transcription	Aorta	Aorta
23	chr15:52245800-52263000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:52245800-52263200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:52246000-52257800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr15:52246400-52262200	Weak transcription	NHLF	lung
27	chr15:52247000-52262400	Weak transcription	Colonic Mucosa	Colon
28	chr15:52249800-52263000	Weak transcription	Psoas Muscle	Psoas
29	chr15:52250400-52258000	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:52250600-52258000	Strong transcription	Primary hematopoietic stem cells	blood
31	chr15:52252200-52258800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:52252800-52257800	Weak transcription	HUVEC	blood vessel
33	chr15:52253200-52256800	Weak transcription	Primary B cells from cord blood	blood
34	chr15:52253200-52257200	Weak transcription	NH-A	brain
35	chr15:52253200-52257600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr15:52253200-52259600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr15:52253200-52259800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr15:52253200-52262400	Weak transcription	Fetal Brain Male	brain
39	chr15:52253200-52262800	Weak transcription	HSMMtube	muscle
40	chr15:52253200-52263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr15:52253400-52259600	Weak transcription	Brain Angular Gyrus	brain
42	chr15:52253400-52262400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr15:52253400-52262400	Weak transcription	Esophagus	oesophagus
44	chr15:52253600-52263000	Weak transcription	Right Ventricle	heart
45	chr15:52253800-52258000	Weak transcription	Brain Substantia Nigra	brain
46	chr15:52253800-52261800	Weak transcription	Small Intestine	intestine
47	chr15:52253800-52262800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr15:52253800-52263200	Weak transcription	Gastric	stomach
49	chr15:52254000-52259200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr15:52254000-52259600	Weak transcription	Brain Anterior Caudate	brain

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