Variant report

Variant	rs2475229
Chromosome Location	chr10:116258384-116258385
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116257493..116259296-chr10:116279810..116281846,2	MCF-7	breast:
2	chr10:116246183..116247727-chr10:116258173..116260732,2	MCF-7	breast:

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1407278	1.00[CHD][hapmap];0.82[MEX][hapmap]
rs2475235	1.00[CEU][hapmap]
rs2497714	1.00[CHD][hapmap]
rs4264082	0.84[AMR][1000 genomes];0.89[EUR][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	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2475229	LPAR1	trans	lymphoblastoid	seeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116214600-116263600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr10:116222200-116264400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr10:116225000-116267200	Weak transcription	Aorta	Aorta
4	chr10:116225600-116278800	Weak transcription	HSMM	muscle
5	chr10:116243000-116286200	Weak transcription	Spleen	Spleen
6	chr10:116245000-116258800	Weak transcription	Colonic Mucosa	Colon
7	chr10:116249600-116264800	Weak transcription	Pancreas	Pancrea
8	chr10:116249800-116259400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr10:116250000-116258400	Weak transcription	Fetal Intestine Small	intestine
10	chr10:116250000-116259400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr10:116250200-116264600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr10:116250200-116265200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr10:116251000-116259000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr10:116251400-116258400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr10:116251400-116259200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr10:116252000-116267200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr10:116252200-116264800	Weak transcription	Brain Substantia Nigra	brain
18	chr10:116252400-116263800	Weak transcription	Hela-S3	cervix
19	chr10:116252600-116258800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr10:116252600-116259400	Weak transcription	Brain Anterior Caudate	brain
21	chr10:116252600-116262800	Weak transcription	Psoas Muscle	Psoas
22	chr10:116252600-116264800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr10:116252600-116264800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr10:116252600-116264800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr10:116252800-116258600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr10:116252800-116259400	Weak transcription	Right Atrium	heart
27	chr10:116253000-116258600	Weak transcription	HMEC	breast
28	chr10:116253000-116258800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr10:116253000-116258800	Weak transcription	NHEK	skin
30	chr10:116253200-116258800	Weak transcription	Fetal Thymus	thymus
31	chr10:116253200-116259400	Weak transcription	Gastric	stomach
32	chr10:116253200-116259400	Weak transcription	Thymus	Thymus
33	chr10:116253200-116264600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr10:116253200-116264800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr10:116253600-116259400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr10:116254000-116258600	Genic enhancers	Primary T cells from cord blood	blood
37	chr10:116255400-116258400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr10:116255400-116258600	Weak transcription	Right Ventricle	heart
39	chr10:116255400-116258800	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr10:116255400-116263000	Weak transcription	Fetal Lung	lung
41	chr10:116255400-116264200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr10:116255400-116264600	Weak transcription	Fetal Kidney	kidney
43	chr10:116255600-116259200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr10:116255600-116259400	Weak transcription	Esophagus	oesophagus
45	chr10:116255600-116259600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr10:116255800-116258600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr10:116255800-116259400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr10:116255800-116259800	Weak transcription	HepG2	liver
49	chr10:116255800-116262600	Weak transcription	Fetal Heart	heart
50	chr10:116256000-116258800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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