Variant report

Variant	rs4151450
Chromosome Location	chr13:48918174-48918175
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48877798..48879447-chr13:48917286..48919351,2	K562	blood:

Variant related genes	Relation type
ENSG00000139687	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10219833	0.81[EUR][1000 genomes]
rs11839271	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12100135	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs12430215	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]
rs12871740	0.83[EUR][1000 genomes]
rs12875750	0.90[CEU][hapmap]
rs1573601	0.90[CEU][hapmap]
rs1951775	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1981434	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1981435	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs198563	0.85[CEU][hapmap]
rs198584	0.85[CEU][hapmap]
rs198590	0.85[CEU][hapmap]
rs198604	0.81[CEU][hapmap]
rs198607	0.85[CEU][hapmap]
rs198612	0.81[CEU][hapmap]
rs198619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs198634	0.83[EUR][1000 genomes]
rs2227311	0.82[YRI][hapmap]
rs2243461	0.81[EUR][1000 genomes]
rs2243626	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs2248488	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs2251813	0.82[EUR][1000 genomes]
rs2254423	0.84[EUR][1000 genomes]
rs3092877	1.00[YRI][hapmap]
rs3803188	0.95[CEU][hapmap]
rs3809328	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs3818455	0.90[CEU][hapmap]
rs3825417	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs399413	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4151510	1.00[YRI][hapmap]
rs4594153	0.84[EUR][1000 genomes]
rs4600372	0.81[EUR][1000 genomes]
rs4942765	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs520342	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs7984554	0.83[EUR][1000 genomes]
rs7984795	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs8001315	0.83[EUR][1000 genomes]
rs9316367	0.90[CEU][hapmap]
rs9316369	0.90[CEU][hapmap]
rs9316381	0.85[CEU][hapmap]
rs9316388	0.85[CEU][hapmap]
rs9316395	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs9316399	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs943278	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9526465	1.00[CEU][hapmap]
rs9526475	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9534998	0.90[CEU][hapmap]
rs9535002	0.84[EUR][1000 genomes]
rs9535006	0.90[CEU][hapmap]
rs9535007	0.84[EUR][1000 genomes]
rs9535009	0.90[CEU][hapmap]
rs9535011	0.81[EUR][1000 genomes]
rs9535015	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535016	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535018	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535032	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9535033	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9562819	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9568029	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9568031	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568032	0.81[EUR][1000 genomes]
rs9568035	0.80[EUR][1000 genomes]
rs9568036	0.84[MKK][hapmap]
rs9568043	0.82[AMR][1000 genomes]
rs990814	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039312	chr13:48898950-48925357	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1038705	chr13:48899219-48922327	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1042504	chr13:48911264-48925357	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4151450	LPAR6	cis	parietal	SCAN
rs4151450	ATAD2	trans	parietal	SCAN
rs4151450	ITM2B	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48880600-48924600	Weak transcription	Psoas Muscle	Psoas
2	chr13:48892600-48927800	Weak transcription	HUVEC	blood vessel
3	chr13:48894600-48919200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr13:48895200-48923600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr13:48895200-48924600	Weak transcription	HSMMtube	muscle
6	chr13:48895400-48924800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr13:48895800-48919600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr13:48895800-48920400	Weak transcription	Right Ventricle	heart
9	chr13:48895800-48926600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr13:48896000-48919800	Weak transcription	Primary T cells from cord blood	blood
11	chr13:48903400-48924400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr13:48908400-48922200	Weak transcription	Liver	Liver
13	chr13:48908400-48944800	Weak transcription	Small Intestine	intestine
14	chr13:48908800-48919200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr13:48908800-48919600	Weak transcription	HMEC	breast
16	chr13:48908800-48927600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr13:48909000-48923600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr13:48909000-48924400	Weak transcription	Osteobl	bone
19	chr13:48909000-48972200	Weak transcription	NHEK	skin
20	chr13:48911800-48919600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr13:48911800-48948400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr13:48912200-48968200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr13:48913200-48919400	Weak transcription	Brain Anterior Caudate	brain
24	chr13:48913200-48924800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr13:48913400-48923400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr13:48913400-48925800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr13:48913400-48944200	Weak transcription	Aorta	Aorta
28	chr13:48913600-48918400	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr13:48913600-48918400	Weak transcription	Left Ventricle	heart
30	chr13:48913800-48919200	Weak transcription	Adipose Nuclei	Adipose
31	chr13:48913800-48923400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr13:48913800-48924800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr13:48913800-48924800	Weak transcription	Thymus	Thymus
34	chr13:48913800-48926200	Weak transcription	Gastric	stomach
35	chr13:48914000-48918400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr13:48914000-48918400	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr13:48914000-48918400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr13:48914000-48920400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr13:48914000-48921200	Weak transcription	Fetal Intestine Small	intestine
40	chr13:48914000-48923400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr13:48914000-48923600	Weak transcription	Fetal Lung	lung
42	chr13:48914000-48924800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr13:48914000-48924800	Weak transcription	Ovary	ovary
44	chr13:48914000-48944400	Weak transcription	Fetal Stomach	stomach
45	chr13:48914000-48965800	Weak transcription	Lung	lung
46	chr13:48914400-48918200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr13:48914400-48918400	Weak transcription	Pancreas	Pancrea
48	chr13:48914400-48919200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr13:48914400-48919200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr13:48914400-48919200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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