Variant report

Variant	rs12430215
Chromosome Location	chr13:48989086-48989087
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr13:48989041-48989143	HepG2	liver:	n/a	n/a
2	MAFK	chr13:48988689-48989149	IMR90	lung:	n/a	chr13:48989036-48989052 chr13:48988835-48988849 chr13:48989034-48989054 chr13:48988837-48988848 chr13:48988837-48988848 chr13:48988836-48988847 chr13:48988836-48988847 chr13:48988832-48988847 chr13:48989037-48989051
3	MAFK	chr13:48988663-48989184	HepG2	liver:	n/a	chr13:48989036-48989052 chr13:48988835-48988849 chr13:48989034-48989054 chr13:48988837-48988848 chr13:48988837-48988848 chr13:48988836-48988847 chr13:48988836-48988847 chr13:48988832-48988847 chr13:48989037-48989051

Variant related genes	Relation type
LPAR6	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11839271	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12100135	0.85[CEU][hapmap]
rs12875750	0.81[CEU][hapmap]
rs1894255	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs1951775	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1981434	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1981435	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs198561	0.81[EUR][1000 genomes]
rs198604	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs198619	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2227311	1.00[YRI][hapmap]
rs2243626	0.86[CEU][hapmap]
rs2248488	0.82[CEU][hapmap]
rs2254423	0.81[EUR][1000 genomes]
rs3092877	0.82[YRI][hapmap]
rs375105	0.83[EUR][1000 genomes]
rs3803188	0.86[CEU][hapmap]
rs3809328	0.85[CEU][hapmap]
rs3825417	0.85[AMR][1000 genomes]
rs399413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4151450	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4151510	0.82[YRI][hapmap]
rs4594153	0.81[EUR][1000 genomes]
rs471911	0.80[EUR][1000 genomes]
rs4942765	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139578	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7984795	0.91[CEU][hapmap]
rs9316369	0.80[CEU][hapmap]
rs9316395	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs9316399	0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.83[YRI][hapmap]
rs943278	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs9526465	0.91[CEU][hapmap]
rs9526475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526479	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs9535002	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9535007	0.81[EUR][1000 genomes]
rs9535015	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535016	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535018	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535032	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535033	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9562819	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568029	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9568031	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9568035	0.90[CEU][hapmap]
rs9568043	0.84[AFR][1000 genomes]
rs990814	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv1053432	chr13:48971510-48992810	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1043486	chr13:48971510-48996995	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12430215	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48976000-49005800	Weak transcription	Hela-S3	cervix
2	chr13:48978400-48989800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr13:48978800-48990400	Weak transcription	Spleen	Spleen
4	chr13:48986600-48990200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:48986600-48990200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:48986600-48990400	Weak transcription	Brain Germinal Matrix	brain
7	chr13:48986600-48990400	Weak transcription	Gastric	stomach
8	chr13:48986600-48990400	Weak transcription	Pancreas	Pancrea
9	chr13:48986800-48990200	Weak transcription	Lung	lung
10	chr13:48987000-48990400	Weak transcription	Fetal Brain Female	brain
11	chr13:48987000-48992800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr13:48987200-48990000	Weak transcription	Placenta	Placenta
13	chr13:48987200-48990200	Weak transcription	Small Intestine	intestine
14	chr13:48987200-48990400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr13:48987200-48993200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr13:48987400-48989800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr13:48987400-48990200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr13:48987400-48990200	Weak transcription	Fetal Stomach	stomach
19	chr13:48987400-48990200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr13:48987400-48990400	Weak transcription	Left Ventricle	heart
21	chr13:48987400-48990600	Weak transcription	Right Ventricle	heart
22	chr13:48987400-48991200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr13:48987400-48991200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr13:48987600-48989400	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr13:48987600-48989400	Enhancers	Primary T cells fromperipheralblood	blood
26	chr13:48987600-48989400	Weak transcription	Fetal Intestine Small	intestine
27	chr13:48987600-48989600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr13:48987600-48989600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr13:48987600-48989800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr13:48987600-48989800	Weak transcription	Primary B cells from cord blood	blood
31	chr13:48987600-48990000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr13:48987600-48990200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr13:48987600-48990200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr13:48987600-48990200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr13:48987600-48990200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr13:48987600-48990200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr13:48987600-48990200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr13:48987600-48990200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr13:48987600-48990200	Weak transcription	Esophagus	oesophagus
40	chr13:48987600-48990200	Weak transcription	Fetal Thymus	thymus
41	chr13:48987600-48990200	Weak transcription	Thymus	Thymus
42	chr13:48987600-48990400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr13:48987600-48990400	Weak transcription	Liver	Liver
44	chr13:48987600-48990400	Weak transcription	Ovary	ovary
45	chr13:48987600-48990600	Weak transcription	NHLF	lung
46	chr13:48987600-48991000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr13:48987600-48991200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr13:48987600-48991200	Weak transcription	HSMMtube	muscle
49	chr13:48987600-48991400	Weak transcription	Fetal Muscle Leg	muscle
50	chr13:48987600-48992800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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