Variant report

Variant	rs12189508
Chromosome Location	chr5:154209494-154209495
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:154209195..154209843-chr5:154222467..154223169,2	MCF-7	breast:
2	chr5:154205913..154219158-chr5:154234172..154242635,38	MCF-7	breast:
3	chr5:154207634..154212086-chr5:154212438..154216728,14	MCF-7	breast:
4	chr5:154209070..154210004-chr5:154224047..154224831,3	MCF-7	breast:
5	chr5:154133318..154137368-chr5:154208082..154212477,8	MCF-7	breast:
6	chr5:154200501..154205115-chr5:154206575..154209973,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155506	Chromatin interaction
ENSG00000155508	Chromatin interaction
ENSG00000170271	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10515727	0.88[EUR][1000 genomes]
rs12186480	0.89[EUR][1000 genomes]
rs12186610	0.85[EUR][1000 genomes]
rs12187572	0.97[EUR][1000 genomes]
rs12187890	0.90[EUR][1000 genomes]
rs12187921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12187934	0.86[EUR][1000 genomes]
rs12187974	0.86[EUR][1000 genomes]
rs12188149	0.92[EUR][1000 genomes]
rs12188498	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12188906	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1421813	0.92[EUR][1000 genomes]
rs1421814	0.92[EUR][1000 genomes]
rs1421815	0.92[EUR][1000 genomes]
rs1421819	0.90[EUR][1000 genomes]
rs17096232	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17116409	0.88[EUR][1000 genomes]
rs17116417	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17116433	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17116455	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17116489	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17116638	0.90[EUR][1000 genomes]
rs17116669	0.84[EUR][1000 genomes]
rs2291780	0.90[EUR][1000 genomes]
rs3776984	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4452598	0.86[EUR][1000 genomes]
rs4626377	0.86[EUR][1000 genomes]
rs55692274	0.90[EUR][1000 genomes]
rs56773390	0.94[EUR][1000 genomes]
rs56895891	0.86[EUR][1000 genomes]
rs61145644	0.86[EUR][1000 genomes]
rs6580123	0.90[EUR][1000 genomes]
rs6865950	0.92[EUR][1000 genomes]
rs6871813	0.86[EUR][1000 genomes]
rs6895588	0.86[EUR][1000 genomes]
rs6895702	0.86[EUR][1000 genomes]
rs73806917	0.97[EUR][1000 genomes]
rs73807206	0.92[EUR][1000 genomes]
rs73807207	0.92[EUR][1000 genomes]
rs73807213	0.90[EUR][1000 genomes]
rs73807216	0.86[EUR][1000 genomes]
rs73809507	0.92[EUR][1000 genomes]
rs7709899	0.92[EUR][1000 genomes]
rs7716019	0.87[AMR][1000 genomes];0.90[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	nsv830521	chr5:154147567-154244266	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 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	chr5:154174000-154212200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:154181000-154211600	Strong transcription	Brain Hippocampus Middle	brain
3	chr5:154182000-154211400	Strong transcription	Left Ventricle	heart
4	chr5:154187000-154211400	Strong transcription	Fetal Stomach	stomach
5	chr5:154191800-154211600	Strong transcription	Adipose Nuclei	Adipose
6	chr5:154193000-154211800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:154195600-154214400	Weak transcription	Small Intestine	intestine
8	chr5:154196000-154229200	Weak transcription	Psoas Muscle	Psoas
9	chr5:154196400-154214000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:154197600-154214400	Weak transcription	HUVEC	blood vessel
11	chr5:154197800-154214400	Weak transcription	Hela-S3	cervix
12	chr5:154198600-154211200	Strong transcription	Stomach Smooth Muscle	stomach
13	chr5:154198600-154211400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:154199400-154214400	Weak transcription	Right Atrium	heart
15	chr5:154200200-154214400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:154200800-154214000	Weak transcription	Fetal Heart	heart
17	chr5:154201000-154228000	Weak transcription	Fetal Brain Male	brain
18	chr5:154203400-154229000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:154203600-154214400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr5:154203800-154210600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:154203800-154211400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr5:154204000-154210000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:154204200-154209600	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr5:154204200-154211000	Weak transcription	Thymus	Thymus
25	chr5:154204200-154214400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr5:154204400-154210000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr5:154204400-154211400	Strong transcription	Liver	Liver
28	chr5:154204400-154213800	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr5:154204400-154213800	Weak transcription	NHDF-Ad	bronchial
30	chr5:154204400-154214400	Weak transcription	Brain Germinal Matrix	brain
31	chr5:154205400-154211400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:154205800-154209800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:154205800-154211400	Strong transcription	Fetal Intestine Small	intestine
34	chr5:154206400-154212800	Strong transcription	Brain Anterior Caudate	brain
35	chr5:154206600-154210600	Enhancers	Primary T cells fromperipheralblood	blood
36	chr5:154206600-154210800	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr5:154206600-154211800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:154206800-154210400	Enhancers	HMEC	breast
39	chr5:154206800-154211000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:154206800-154211000	Strong transcription	Brain Cingulate Gyrus	brain
41	chr5:154206800-154211000	Strong transcription	Fetal Lung	lung
42	chr5:154206800-154211400	Genic enhancers	HepG2	liver
43	chr5:154207000-154211400	Strong transcription	Brain Substantia Nigra	brain
44	chr5:154207200-154210000	Strong transcription	Placenta	Placenta
45	chr5:154207200-154210200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:154207200-154210800	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr5:154207200-154211400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:154207200-154211400	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr5:154207200-154211600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:154207400-154210800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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