Variant report

Variant	rs12553
Chromosome Location	chr5:178315968-178315969
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178310967..178313055-chr5:178314057..178317226,3	MCF-7	breast:
2	chr5:178314966..178317801-chr5:178321245..178325821,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198939	Chromatin interaction
ENSG00000206624	Chromatin interaction
ENSG00000178338	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10039708	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11249599	0.81[EUR][1000 genomes]
rs11948175	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11948664	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11948690	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11949180	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11949181	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11949892	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11949941	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11950641	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11950746	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11952790	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11954382	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11955047	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11958804	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11958887	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11958941	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11960942	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12186577	0.83[EUR][1000 genomes]
rs12186584	0.84[EUR][1000 genomes]
rs12187167	0.84[EUR][1000 genomes]
rs1566106	0.94[EUR][1000 genomes]
rs28539861	0.82[EUR][1000 genomes]
rs35609799	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35957383	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56814168	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56872885	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56932649	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56951084	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57153194	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57426447	0.94[EUR][1000 genomes]
rs58354049	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58554591	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58672680	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58679434	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58941917	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59242428	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59736551	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59829327	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59849584	0.84[EUR][1000 genomes]
rs59994898	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60178472	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60277514	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60417551	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60601817	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60813042	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61295075	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61310482	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61492890	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61744382	0.84[EUR][1000 genomes]
rs62395084	0.82[EUR][1000 genomes]
rs6600991	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6859174	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6861717	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6863160	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6863202	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6863603	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6865216	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6866591	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6870926	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6877663	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6878353	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6882396	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6883566	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6887256	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6890083	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6894878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6895371	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7706558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7724141	0.83[EUR][1000 genomes]
rs7727497	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7729560	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7729717	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7731067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178288200-178317400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
2	chr5:178288800-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:178289600-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr5:178291200-178317400	ZNF genes & repeats	Liver	Liver
5	chr5:178296000-178319200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
6	chr5:178296200-178319200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:178296400-178317600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
8	chr5:178297400-178317400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:178297400-178317400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
10	chr5:178297400-178317400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:178297600-178317400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:178298800-178317800	ZNF genes & repeats	Primary T cells from cord blood	blood
13	chr5:178299000-178317600	ZNF genes & repeats	Fetal Brain Female	brain
14	chr5:178299400-178317400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:178299600-178317400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
16	chr5:178299800-178317400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:178299800-178317600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:178301000-178317400	ZNF genes & repeats	Adipose Nuclei	Adipose
19	chr5:178301400-178317200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:178301600-178317600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:178302800-178317600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:178305200-178317000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:178306000-178317600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
24	chr5:178306200-178317600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:178307400-178317600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
26	chr5:178307600-178317400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:178307600-178317400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
28	chr5:178307600-178317600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
29	chr5:178308400-178322600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr5:178308800-178316000	Strong transcription	Placenta	Placenta
31	chr5:178308800-178316400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr5:178311200-178316600	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:178311200-178322400	Weak transcription	Hela-S3	cervix
34	chr5:178312200-178317600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
35	chr5:178312400-178317600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
36	chr5:178312600-178316200	ZNF genes & repeats	NH-A	brain
37	chr5:178312800-178317400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:178313200-178316000	Weak transcription	NHLF	lung
39	chr5:178313200-178316400	Weak transcription	Right Ventricle	heart
40	chr5:178313200-178317200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:178313400-178316600	Weak transcription	K562	blood
42	chr5:178313600-178316400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:178313600-178316600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr5:178313600-178317200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr5:178313600-178322600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr5:178313600-178322800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr5:178313800-178316400	Weak transcription	Fetal Thymus	thymus
48	chr5:178313800-178316400	Weak transcription	NHDF-Ad	bronchial
49	chr5:178313800-178316800	Weak transcription	Fetal Heart	heart
50	chr5:178313800-178316800	Strong transcription	Skeletal Muscle Female	skeletal muscle

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