Variant report

Variant	rs2623273
Chromosome Location	chr15:52166025-52166026
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52163617..52167105-chr15:52168428..52170438,3	MCF-7	breast:
2	chr15:51913874..51916144-chr15:52165568..52168116,2	MCF-7	breast:
3	chr15:52119461..52123475-chr15:52166022..52168353,4	MCF-7	breast:
4	chr15:52165419..52167687-chr15:52262244..52264140,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction
ENSG00000104093	Chromatin interaction
ENSG00000166477	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs11446467	0.83[AFR][1000 genomes]
rs1426085	0.81[AFR][1000 genomes]
rs1867985	0.87[AFR][1000 genomes]
rs2162224	0.81[AFR][1000 genomes]
rs2263946	0.81[AFR][1000 genomes]
rs2436663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2436664	0.87[AFR][1000 genomes]
rs2470606	0.84[AFR][1000 genomes]
rs2554311	0.81[AFR][1000 genomes]
rs2554312	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554319	0.93[AFR][1000 genomes]
rs2554320	0.93[AFR][1000 genomes]
rs2554323	0.81[AFR][1000 genomes]
rs2554324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554325	0.84[AFR][1000 genomes]
rs2554329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554330	0.85[AFR][1000 genomes]
rs2554333	0.85[AFR][1000 genomes]
rs2554344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554346	0.87[AFR][1000 genomes]
rs2554351	0.87[AFR][1000 genomes]
rs2554352	0.85[AFR][1000 genomes]
rs2554356	0.87[AFR][1000 genomes]
rs2554357	0.85[AFR][1000 genomes]
rs2570218	0.82[AFR][1000 genomes]
rs2570220	0.81[AFR][1000 genomes]
rs2570221	0.81[AFR][1000 genomes]
rs2570222	0.93[AFR][1000 genomes]
rs2570223	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2570227	0.84[AFR][1000 genomes]
rs2570242	0.87[AFR][1000 genomes]
rs2570244	0.85[AFR][1000 genomes]
rs2570245	0.87[AFR][1000 genomes]
rs2570246	0.81[AFR][1000 genomes]
rs2570247	0.87[AFR][1000 genomes]
rs2570249	0.87[AFR][1000 genomes]
rs2570250	0.87[AFR][1000 genomes]
rs2570256	0.87[AFR][1000 genomes]
rs2570257	0.87[AFR][1000 genomes]
rs2570259	0.83[AFR][1000 genomes]
rs2570261	0.87[AFR][1000 genomes]
rs2570266	0.93[AFR][1000 genomes]
rs2570267	0.81[AFR][1000 genomes]
rs2570272	0.87[AFR][1000 genomes]
rs2570273	0.81[AFR][1000 genomes]
rs2593165	0.81[AFR][1000 genomes]
rs2593171	0.93[AFR][1000 genomes]
rs2593172	0.93[AFR][1000 genomes]
rs2593175	0.81[AFR][1000 genomes]
rs2593176	0.81[AFR][1000 genomes]
rs2593178	0.90[AFR][1000 genomes]
rs2593180	0.81[AFR][1000 genomes]
rs2593186	0.87[AFR][1000 genomes]
rs2593203	0.84[AFR][1000 genomes]
rs2623246	0.87[AFR][1000 genomes]
rs2623248	0.87[AFR][1000 genomes]
rs2623250	0.87[AFR][1000 genomes]
rs2623252	0.87[AFR][1000 genomes]
rs2623264	0.81[AFR][1000 genomes]
rs2623267	0.84[AFR][1000 genomes]
rs2623269	0.87[AFR][1000 genomes]
rs2623274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2623275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2623277	0.81[AFR][1000 genomes]
rs2623278	0.81[AFR][1000 genomes]
rs2623287	0.81[AFR][1000 genomes]
rs2623290	0.93[AFR][1000 genomes]
rs2916174	0.81[AFR][1000 genomes]
rs73396698	0.81[AFR][1000 genomes]
rs73411105	0.87[AFR][1000 genomes]
rs919056	0.84[AFR][1000 genomes]
rs919058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52141600-52166800	Weak transcription	Stomach Mucosa	stomach
2	chr15:52141800-52176200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:52145800-52176600	Weak transcription	Psoas Muscle	Psoas
4	chr15:52148200-52176200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:52149400-52171000	Weak transcription	Brain Angular Gyrus	brain
6	chr15:52149800-52168000	Weak transcription	Right Ventricle	heart
7	chr15:52152400-52170000	Weak transcription	Pancreas	Pancrea
8	chr15:52152400-52170800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:52153800-52178000	Weak transcription	Brain Germinal Matrix	brain
10	chr15:52154400-52170200	Weak transcription	Fetal Brain Male	brain
11	chr15:52155000-52167600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:52155000-52167800	Strong transcription	Primary B cells from peripheral blood	blood
13	chr15:52155000-52169800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr15:52155000-52170800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr15:52155000-52173600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr15:52155200-52167800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr15:52155200-52169600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr15:52155200-52170600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr15:52155600-52166400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr15:52155600-52192000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr15:52156000-52211000	Weak transcription	Brain Substantia Nigra	brain
22	chr15:52156400-52170600	Weak transcription	Brain Anterior Caudate	brain
23	chr15:52156800-52170000	Weak transcription	Spleen	Spleen
24	chr15:52157000-52166800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr15:52157000-52168600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr15:52157000-52170200	Weak transcription	Gastric	stomach
27	chr15:52157000-52170400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr15:52157000-52170800	Weak transcription	Fetal Kidney	kidney
29	chr15:52157200-52167000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr15:52157400-52166800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:52157600-52167400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr15:52157800-52166800	Weak transcription	Colonic Mucosa	Colon
33	chr15:52157800-52178000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr15:52158000-52167000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr15:52158000-52170800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr15:52158200-52168200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr15:52159000-52168600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr15:52159200-52166800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr15:52159400-52166600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr15:52159600-52171000	Weak transcription	Fetal Brain Female	brain
41	chr15:52159800-52167600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr15:52160000-52169400	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr15:52161200-52168800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:52161400-52169200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr15:52161600-52166400	Weak transcription	HUVEC	blood vessel
46	chr15:52161600-52166800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:52161600-52176000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:52161800-52166200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:52161800-52168400	Strong transcription	GM12878-XiMat	blood
50	chr15:52162200-52166600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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