Variant report

Variant	rs17576472
Chromosome Location	chr2:38903022-38903023
allele	A/T
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	POLR2A	chr2:38902970-38903046	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:38902106..38905477-chr2:38907505..38910142,3	K562	blood:
2	chr2:38825670..38832919-chr2:38891527..38903424,21	K562	blood:
3	chr2:38893261..38895190-chr2:38902040..38904878,2	K562	blood:

Variant related genes	Relation type
ENSG00000232518	TF binding region
ENSG00000235586	Chromatin interaction
ENSG00000143891	Chromatin interaction
ENSG00000143889	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12469458	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12469534	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12478924	0.85[ASN][1000 genomes]
rs12712612	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12987870	1.00[CEU][hapmap]
rs13004674	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13004806	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13004842	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13005073	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13006376	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs13010022	0.87[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13011383	0.95[ASN][1000 genomes]
rs13012704	0.93[EUR][1000 genomes]
rs13016907	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13029674	0.86[ASN][1000 genomes]
rs13032255	0.97[ASN][1000 genomes]
rs13383762	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]
rs13425086	0.91[ASN][1000 genomes]
rs17576507	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2373424	0.85[ASN][1000 genomes]
rs28716236	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34391548	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34533539	0.85[ASN][1000 genomes]
rs34558770	0.90[EUR][1000 genomes]
rs34756536	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34875979	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34909144	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35448554	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35585199	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770680	1.00[ASW][hapmap]
rs4670262	0.82[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4670885	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58757994	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6707543	0.97[ASN][1000 genomes]
rs6736380	0.97[ASN][1000 genomes]
rs6741892	0.87[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.83[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
rs17576472	LAP3	trans	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38894000-38904200	Weak transcription	Esophagus	oesophagus
2	chr2:38894000-38904400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:38894000-38917600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:38894200-38903200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:38894200-38903400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:38894200-38904000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:38894200-38904000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:38894200-38904000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:38894200-38904600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:38894200-38906800	Weak transcription	Brain Angular Gyrus	brain
11	chr2:38894200-38919000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:38894400-38903200	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:38894400-38903800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:38894400-38903800	Weak transcription	Right Ventricle	heart
15	chr2:38894400-38904000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:38894400-38904000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:38894400-38904000	Weak transcription	Placenta	Placenta
18	chr2:38894400-38908600	Weak transcription	Brain Anterior Caudate	brain
19	chr2:38894400-38910400	Weak transcription	Psoas Muscle	Psoas
20	chr2:38894400-38917600	Weak transcription	NHDF-Ad	bronchial
21	chr2:38894400-38960600	Weak transcription	Brain Substantia Nigra	brain
22	chr2:38894600-38903200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:38894600-38903200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:38894600-38903200	Weak transcription	Primary B cells from cord blood	blood
25	chr2:38894600-38908000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:38894600-38919600	Weak transcription	Fetal Heart	heart
27	chr2:38894800-38949400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr2:38895000-38917600	Weak transcription	HSMM	muscle
29	chr2:38895200-38903200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:38895200-38908600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:38895600-38903200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr2:38895600-38904400	Weak transcription	Stomach Mucosa	stomach
33	chr2:38895600-38904400	Weak transcription	Hela-S3	cervix
34	chr2:38895600-38906800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:38895600-38912400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr2:38895800-38904000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:38897800-38904400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:38898000-38903200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:38898000-38904400	Weak transcription	A549	lung
40	chr2:38898600-38904400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr2:38898600-38906800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:38898600-38908200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr2:38898600-38912400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:38898600-38921200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr2:38898800-38903200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:38898800-38903200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr2:38898800-38911600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr2:38899000-38903200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr2:38900800-38904200	Weak transcription	Small Intestine	intestine
50	chr2:38901400-38917000	Weak transcription	HSMMtube	muscle

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