Variant report

Variant	rs2936193
Chromosome Location	chr5:58331441-58331442
allele	G/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	chr5:58331302-58331689	MCF10A-Er-Src	breast:	n/a	n/a
2	EP300	chr5:58330146-58332769	SK-N-SH	brain:	n/a	chr5:58332292-58332306
3	GATA3	chr5:58331309-58332669	SK-N-SH	brain:	n/a	chr5:58332250-58332259
4	CEBPZ	chr5:58331381-58331558	HepG2	liver:	n/a	n/a
5	SIX5	chr5:58330273-58336780	A549	lung:	n/a	chr5:58334021-58334030
6	REST	chr5:58331372-58337614	A549	lung:	n/a	chr5:58334044-58334052 chr5:58335557-58335570
7	GATA3	chr5:58331374-58331971	SK-N-SH	brain:	n/a	n/a
8	BCL3	chr5:58330017-58334935	A549	lung:	n/a	chr5:58332249-58332258 chr5:58333393-58333401
9	TCF12	chr5:58331315-58332650	SK-N-SH	brain:	n/a	n/a
10	GATA3	chr5:58330035-58338800	A549	lung:	n/a	chr5:58333570-58333591 chr5:58332852-58332859 chr5:58333577-58333587 chr5:58333577-58333584 chr5:58332250-58332259 chr5:58333577-58333584 chr5:58332852-58332859 chr5:58333577-58333584 chr5:58333572-58333588 chr5:58336798-58336814 chr5:58332852-58332859
11	TCF12	chr5:58331291-58337478	A549	lung:	n/a	chr5:58336418-58336428 chr5:58336399-58336408
12	CHD1	chr5:58331417-58336301	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000247345	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10043357	0.81[CHB][hapmap]
rs10074854	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs10461657	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs1463816	0.83[EUR][1000 genomes]
rs1498599	0.81[CHB][hapmap]
rs1553114	1.00[CEU][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs2936190	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2936192	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936199	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2968006	0.89[ASW][hapmap];0.93[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2968013	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2968014	0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2968015	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2968021	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs3805553	0.93[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs3805554	0.81[EUR][1000 genomes]
rs3805556	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs3805557	1.00[CEU][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs4321723	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4629551	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs4699930	0.93[CEU][hapmap];0.90[CHB][hapmap];0.83[EUR][1000 genomes]
rs4699931	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[EUR][1000 genomes]
rs4700314	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs6450496	1.00[CEU][hapmap]
rs6875727	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7712725	1.00[CEU][hapmap]
rs7713069	0.93[CEU][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs7713345	1.00[CEU][hapmap]
rs7724713	0.93[CEU][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs7737685	1.00[CEU][hapmap];0.82[EUR][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	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1032308	chr5:58312468-58371239	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2936193	PDE4D	cis	lymphoblastoid	seeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58313000-58333400	Weak transcription	Lung	lung
2	chr5:58317200-58331600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:58317800-58331800	Weak transcription	Fetal Intestine Small	intestine
4	chr5:58318000-58333000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr5:58318600-58333000	Weak transcription	Left Ventricle	heart
6	chr5:58318600-58333200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:58320200-58334600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:58321800-58334000	Weak transcription	Gastric	stomach
9	chr5:58322000-58331800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr5:58324600-58333000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr5:58326000-58332200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:58327000-58334000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:58329200-58331800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr5:58329200-58332400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr5:58329200-58333200	Enhancers	Rectal Smooth Muscle	rectum
16	chr5:58330000-58331600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:58330000-58331600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:58330000-58332000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:58330200-58331600	Enhancers	Muscle Satellite Cultured Cells	--
20	chr5:58330200-58331600	Enhancers	NHEK	skin
21	chr5:58330200-58331800	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr5:58330200-58331800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr5:58330200-58332200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr5:58330200-58332200	Enhancers	Fetal Lung	lung
25	chr5:58330200-58333000	Enhancers	Primary hematopoietic stem cells	blood
26	chr5:58330200-58333600	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr5:58330400-58331600	Enhancers	Placenta Amnion	Placenta Amnion
28	chr5:58330400-58331800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr5:58330400-58332200	Enhancers	Colon Smooth Muscle	Colon
30	chr5:58330400-58336400	Active TSS	Right Ventricle	heart
31	chr5:58330400-58336600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
32	chr5:58330600-58332000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr5:58330600-58332000	Genic enhancers	Hela-S3	cervix
34	chr5:58330600-58332200	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr5:58330600-58332400	Enhancers	HSMMtube	muscle
36	chr5:58330600-58333400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:58330600-58333600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:58330600-58334600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:58330600-58335000	Transcr. at gene 5' and 3'	A549	lung
40	chr5:58330600-58336200	Active TSS	Right Atrium	heart
41	chr5:58330800-58331600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:58330800-58331800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:58330800-58331800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr5:58330800-58331800	Enhancers	HepG2	liver
45	chr5:58330800-58331800	Enhancers	NHDF-Ad	bronchial
46	chr5:58330800-58333000	Active TSS	Thymus	Thymus
47	chr5:58330800-58335800	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr5:58331000-58331600	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr5:58331000-58331600	Enhancers	HSMM	muscle
50	chr5:58331000-58331600	Enhancers	Osteobl	bone

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