Variant report

Variant	rs9364
Chromosome Location	chr12:50570519-50570520
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50496386..50497971-chr12:50569174..50571228,2	MCF-7	breast:
2	chr12:50471994..50474538-chr12:50569711..50571544,2	MCF-7	breast:
3	chr12:50479656..50481335-chr12:50569381..50571958,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167588	Chromatin interaction
ENSG00000110881	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10783338	0.84[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs10876000	0.82[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap]
rs10876023	0.83[JPT][hapmap]
rs11169281	0.82[CEU][hapmap];0.85[CHB][hapmap]
rs11169282	0.88[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap]
rs11169302	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12424335	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1554844	0.88[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap]
rs1554845	0.80[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap]
rs17124432	0.88[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap]
rs17124514	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs3184122	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34145380	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34245511	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34309034	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3741562	0.88[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap]
rs6580728	0.88[CEU][hapmap]
rs7138420	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7138622	0.85[ASN][1000 genomes]
rs7138945	0.85[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap]
rs7294618	0.88[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7307230	0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs7308474	0.82[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap]
rs7315690	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7398567	0.85[ASN][1000 genomes]
rs7961065	0.88[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7961112	0.88[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7967979	0.80[CEU][hapmap]
rs7968119	0.82[CEU][hapmap]
rs7972465	0.88[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs7978904	0.81[ASN][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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9364	CERS5	cis	Nerve Tibial	GTEx
rs9364	KIAA1463	cis	multi-tissue	Pritchard
rs9364	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs9364	CERS5	cis	Muscle Skeletal	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50561200-50570600	Weak transcription	Aorta	Aorta
2	chr12:50561600-50570600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:50561600-50570800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:50561600-50570800	Weak transcription	Esophagus	oesophagus
5	chr12:50561600-50570800	Weak transcription	Gastric	stomach
6	chr12:50561600-50570800	Weak transcription	Pancreas	Pancrea
7	chr12:50561600-50571200	Weak transcription	Lung	lung
8	chr12:50561600-50571200	Weak transcription	Right Ventricle	heart
9	chr12:50561600-50575200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:50561800-50570600	Weak transcription	Primary T cells from cord blood	blood
11	chr12:50561800-50570600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr12:50561800-50570800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:50561800-50570800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr12:50561800-50570800	Weak transcription	Brain Angular Gyrus	brain
15	chr12:50561800-50570800	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:50561800-50570800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:50561800-50570800	Weak transcription	Ovary	ovary
18	chr12:50561800-50571000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:50561800-50571000	Weak transcription	Colonic Mucosa	Colon
20	chr12:50561800-50571000	Weak transcription	Spleen	Spleen
21	chr12:50561800-50571200	Weak transcription	Brain Germinal Matrix	brain
22	chr12:50561800-50571200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:50561800-50571200	Weak transcription	Left Ventricle	heart
24	chr12:50561800-50571200	Weak transcription	Thymus	Thymus
25	chr12:50561800-50573000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr12:50561800-50574800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr12:50561800-50574800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr12:50561800-50575000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:50561800-50582600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr12:50561800-50582600	Weak transcription	Stomach Mucosa	stomach
31	chr12:50562000-50570600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr12:50562000-50570600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr12:50562000-50570600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr12:50562000-50570600	Weak transcription	Fetal Thymus	thymus
35	chr12:50562000-50570800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:50562000-50571000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:50562000-50571000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:50562000-50571400	Weak transcription	Fetal Lung	lung
39	chr12:50562000-50576000	Weak transcription	Fetal Heart	heart
40	chr12:50562000-50576400	Weak transcription	A549	lung
41	chr12:50562000-50584800	Weak transcription	K562	blood
42	chr12:50562200-50597000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:50564400-50570800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:50564400-50586200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr12:50564400-50600800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr12:50564600-50571000	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr12:50564600-50571200	Weak transcription	HepG2	liver
48	chr12:50566000-50570800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr12:50566200-50570800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr12:50566400-50571200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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