Variant report

Variant	rs13383762
Chromosome Location	chr2:38907001-38907002
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38827534..38829774-chr2:38906960..38909388,3	K562	blood:
2	chr2:38892930..38895051-chr2:38905642..38907216,2	K562	blood:
3	chr2:38897993..38900823-chr2:38904497..38907341,3	K562	blood:

Variant related genes	Relation type
ENSG00000232518	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000143891	Chromatin interaction
ENSG00000235586	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12469458	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12469534	0.87[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12478924	0.85[ASN][1000 genomes]
rs12712612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12987870	0.87[CEU][hapmap];0.85[GIH][hapmap]
rs13004674	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13004806	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13004842	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13005073	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13006376	0.85[CEU][hapmap];0.97[EUR][1000 genomes]
rs13010022	1.00[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13011383	0.93[ASN][1000 genomes]
rs13012704	0.95[EUR][1000 genomes]
rs13016907	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13029674	0.86[ASN][1000 genomes]
rs13032255	0.95[ASN][1000 genomes]
rs13425086	0.89[ASN][1000 genomes]
rs17576472	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17576507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2373424	0.85[ASN][1000 genomes]
rs28716236	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34391548	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34533539	0.83[ASN][1000 genomes]
rs34558770	0.88[EUR][1000 genomes]
rs34756536	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34875979	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34909144	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35448554	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35585199	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4670262	0.82[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs4670885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58757994	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6707543	0.95[ASN][1000 genomes]
rs6736380	0.95[ASN][1000 genomes]
rs6741892	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873882	chr2:38858669-38921498	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv873883	chr2:38881106-38932777	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13383762	LAP3	trans	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38894000-38917600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:38894200-38919000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:38894400-38908600	Weak transcription	Brain Anterior Caudate	brain
4	chr2:38894400-38910400	Weak transcription	Psoas Muscle	Psoas
5	chr2:38894400-38917600	Weak transcription	NHDF-Ad	bronchial
6	chr2:38894400-38960600	Weak transcription	Brain Substantia Nigra	brain
7	chr2:38894600-38908000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:38894600-38919600	Weak transcription	Fetal Heart	heart
9	chr2:38894800-38949400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:38895000-38917600	Weak transcription	HSMM	muscle
11	chr2:38895200-38908600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:38895600-38912400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:38898600-38908200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:38898600-38912400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:38898600-38921200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:38898800-38911600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:38901400-38917000	Weak transcription	HSMMtube	muscle
18	chr2:38902400-38908800	Strong transcription	Primary T cells from cord blood	blood
19	chr2:38902800-38916600	Strong transcription	Fetal Stomach	stomach
20	chr2:38903000-38907200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr2:38903000-38907600	Strong transcription	Ovary	ovary
22	chr2:38903000-38908800	Strong transcription	Thymus	Thymus
23	chr2:38903000-38909200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:38903000-38909200	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:38903000-38909400	Strong transcription	Primary B cells from peripheral blood	blood
26	chr2:38903000-38909400	Strong transcription	Osteobl	bone
27	chr2:38903000-38909600	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:38903000-38909600	Strong transcription	Fetal Lung	lung
29	chr2:38903000-38909600	Strong transcription	Stomach Smooth Muscle	stomach
30	chr2:38903000-38909800	Strong transcription	Fetal Muscle Trunk	muscle
31	chr2:38903000-38912200	Strong transcription	Fetal Muscle Leg	muscle
32	chr2:38903000-38912400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:38903000-38912800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:38903200-38907200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:38903200-38910400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:38903200-38910600	Strong transcription	Primary B cells from cord blood	blood
37	chr2:38903200-38912800	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr2:38903400-38908400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:38903400-38910600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:38903600-38923800	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:38903800-38918600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr2:38904000-38909200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:38904400-38918400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr2:38904600-38908400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr2:38904800-38908400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:38904800-38936000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr2:38905000-38907400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:38905000-38907800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr2:38905000-38908000	Weak transcription	Aorta	Aorta
50	chr2:38905000-38908000	Weak transcription	Fetal Kidney	kidney

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