Variant report

Variant	rs1412445
Chromosome Location	chr10:91002804-91002805
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:91001026..91003568-chr10:91009679..91012651,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000107798	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1051338	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1332328	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1332329	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1412444	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2243547	0.84[EUR][1000 genomes]
rs2246828	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2246833	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2246941	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2246942	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2250644	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2250645	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv2758235	chr10:90835064-91017486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv2759775	chr10:90835064-91017486	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1041964	chr10:90861380-91378356	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1412445	LIPA	cis	Whole Blood	GTEx
rs1412445	LIPA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90977400-91010400	Weak transcription	Fetal Thymus	thymus
2	chr10:90977400-91010800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr10:90977600-91008800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr10:90977600-91009400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr10:90977600-91010400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr10:90977600-91010800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr10:90979400-91003600	Strong transcription	Primary T cells from cord blood	blood
8	chr10:90985200-91010600	Weak transcription	Thymus	Thymus
9	chr10:90987400-91010800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr10:90987600-91010800	Weak transcription	Pancreas	Pancrea
11	chr10:90987800-91010600	Weak transcription	HSMM	muscle
12	chr10:90988000-91010600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr10:90989200-91003200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr10:90994800-91010800	Weak transcription	Esophagus	oesophagus
15	chr10:90995600-91003000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:90998600-91004200	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr10:90998800-91003200	Strong transcription	Stomach Smooth Muscle	stomach
18	chr10:90999000-91004200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr10:90999600-91005400	Weak transcription	Brain Angular Gyrus	brain
20	chr10:90999600-91010400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr10:90999800-91010000	Weak transcription	Dnd41	blood
22	chr10:90999800-91010400	Weak transcription	Colon Smooth Muscle	Colon
23	chr10:90999800-91010400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr10:90999800-91010600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr10:90999800-91010600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr10:90999800-91010800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr10:90999800-91010800	Weak transcription	Ovary	ovary
28	chr10:91000000-91004800	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr10:91000000-91010400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr10:91000000-91010600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr10:91000200-91003200	Enhancers	Placenta	Placenta
32	chr10:91000200-91010600	Weak transcription	Brain Germinal Matrix	brain
33	chr10:91000200-91010600	Weak transcription	Fetal Brain Female	brain
34	chr10:91000400-91003600	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr10:91000600-91003000	Enhancers	Liver	Liver
36	chr10:91000600-91010400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr10:91000600-91010800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr10:91000800-91003200	Genic enhancers	Brain Anterior Caudate	brain
39	chr10:91000800-91003600	Enhancers	H9 Cell Line	embryonic stem cell
40	chr10:91000800-91004200	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr10:91001000-91003000	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr10:91001000-91003600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr10:91001000-91003800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr10:91001000-91010600	Weak transcription	Fetal Stomach	stomach
45	chr10:91001000-91010600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr10:91001200-91003200	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr10:91001200-91003200	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr10:91001200-91006400	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr10:91001200-91009400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr10:91001200-91010600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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