Variant report

Variant	rs12623380
Chromosome Location	chr2:54136714-54136715
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:72115529..72117582-chr2:54136629..54139608,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10210726	0.87[CEU][hapmap]
rs10432674	0.88[ASN][1000 genomes]
rs12162342	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12162343	0.91[ASN][1000 genomes]
rs12612589	0.87[CEU][hapmap]
rs12613682	0.87[CEU][hapmap]
rs12614854	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12618587	0.84[EUR][1000 genomes]
rs12620190	0.84[EUR][1000 genomes]
rs12620208	0.84[EUR][1000 genomes]
rs12620383	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12621635	0.87[CEU][hapmap]
rs12621783	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12623273	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1547980	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17045215	0.87[CEU][hapmap]
rs17045292	0.86[EUR][1000 genomes]
rs17045337	0.87[ASN][1000 genomes]
rs17045370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17045386	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17045435	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2068017	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs2272250	0.82[EUR][1000 genomes]
rs2287344	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs2287345	0.84[EUR][1000 genomes]
rs2293361	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28396307	0.88[ASN][1000 genomes]
rs3213775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3731972	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3731973	0.94[CHB][hapmap];0.88[ASN][1000 genomes]
rs3770389	0.94[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3770401	0.87[CEU][hapmap]
rs3821078	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3850347	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6713523	0.89[CHB][hapmap];0.88[ASN][1000 genomes]
rs6720298	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72799229	0.84[EUR][1000 genomes]
rs72799234	0.84[EUR][1000 genomes]
rs72799236	0.81[EUR][1000 genomes]
rs72799239	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72799248	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72799250	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72799257	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs72799259	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72799262	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72799268	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7580916	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7595713	0.87[CEU][hapmap]
rs7600276	0.82[EUR][1000 genomes]
rs805371	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9309252	0.86[ASN][1000 genomes]

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54087000-54168000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr2:54087200-54176000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:54087400-54137600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:54087600-54187600	Weak transcription	Stomach Mucosa	stomach
5	chr2:54088400-54137200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:54088600-54138000	Strong transcription	Primary B cells from peripheral blood	blood
7	chr2:54090200-54137800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:54090200-54138200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:54090400-54137600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:54090800-54137400	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr2:54091000-54137000	Strong transcription	Fetal Thymus	thymus
12	chr2:54091000-54137800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:54091000-54138000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:54091200-54138000	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr2:54091400-54137600	Strong transcription	Liver	Liver
16	chr2:54094000-54137800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:54099200-54137400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:54100400-54137800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:54100400-54137800	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr2:54100400-54140200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr2:54100600-54137400	Strong transcription	Placenta	Placenta
22	chr2:54100600-54137800	Strong transcription	Primary B cells from cord blood	blood
23	chr2:54100600-54141200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:54100800-54138000	Strong transcription	Fetal Muscle Trunk	muscle
25	chr2:54105800-54137200	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr2:54106000-54138000	Strong transcription	Dnd41	blood
27	chr2:54106200-54138400	Strong transcription	Adipose Nuclei	Adipose
28	chr2:54106600-54137800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr2:54108200-54137400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:54108200-54177400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:54108400-54137400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:54108600-54137800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:54108800-54137400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:54109400-54137200	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr2:54109400-54137400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr2:54109400-54137400	Strong transcription	Fetal Lung	lung
37	chr2:54109400-54137600	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:54109400-54137800	Strong transcription	NH-A	brain
39	chr2:54109800-54179800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr2:54111200-54137600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:54113200-54144600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr2:54121800-54137400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:54122200-54172800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr2:54124400-54159200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr2:54124600-54137400	Strong transcription	Fetal Intestine Large	intestine
46	chr2:54124800-54137600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:54124800-54137600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:54124800-54137600	Strong transcription	HSMM	muscle
49	chr2:54124800-54140800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:54124800-54141000	Strong transcription	Osteobl	bone

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