Variant report

Variant	rs4670745
Chromosome Location	chr2:37863583-37863584
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-QPCT-3	chr2:37832379-37870742	NONHSAT070127

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1013292	0.81[AMR][1000 genomes]
rs10694	0.84[MEX][hapmap]
rs13406302	0.86[JPT][hapmap]
rs13417833	0.88[ASN][1000 genomes]
rs13417957	0.82[ASN][1000 genomes]
rs2072419	0.86[JPT][hapmap]
rs2373292	0.88[ASN][1000 genomes]
rs3731852	0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs3731854	0.81[JPT][hapmap];0.82[AMR][1000 genomes]
rs4670210	0.81[JPT][hapmap]
rs4670748	0.81[JPT][hapmap]
rs62135589	0.86[ASN][1000 genomes]
rs6752220	0.86[JPT][hapmap]
rs6759224	0.81[JPT][hapmap]
rs727805	0.80[ASN][1000 genomes]
rs7735	0.86[JPT][hapmap];0.83[MEX][hapmap]
rs9742	0.88[ASW][hapmap];0.86[JPT][hapmap];0.80[LWK][hapmap];0.84[MEX][hapmap];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456374	chr2:37669487-37868214	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv470453	chr2:37669487-37868214	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv581473	chr2:37669487-37868214	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2757793	chr2:37796654-38138939	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	esv2759043	chr2:37796654-38138939	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv833825	chr2:37808169-37985917	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv535645	chr2:37853282-37972640	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv535646	chr2:37853282-38014428	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4670745	CDC42EP3	cis	lymphoblastoid	seeQTL
rs4670745	CDC42EP3	cis	multi-tissue	Pritchard

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37853600-37873200	Weak transcription	Liver	Liver
2	chr2:37853600-37897400	Weak transcription	Small Intestine	intestine
3	chr2:37857000-37871400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:37857200-37865200	Weak transcription	Left Ventricle	heart
5	chr2:37857200-37865800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:37857200-37868200	Weak transcription	Psoas Muscle	Psoas
7	chr2:37858000-37868600	Weak transcription	A549	lung
8	chr2:37858400-37867600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:37858800-37871400	Weak transcription	Aorta	Aorta
10	chr2:37859000-37868600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:37859200-37868600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:37859600-37865000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:37859800-37864200	Weak transcription	Fetal Heart	heart
14	chr2:37860000-37863600	Weak transcription	HSMMtube	muscle
15	chr2:37860000-37871200	Weak transcription	Gastric	stomach
16	chr2:37860200-37864800	Enhancers	Primary hematopoietic stem cells	blood
17	chr2:37860200-37864800	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr2:37860200-37866800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr2:37860200-37868600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:37860400-37864800	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr2:37860400-37865600	Enhancers	Primary T cells fromperipheralblood	blood
22	chr2:37860400-37865600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:37860400-37867400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr2:37860800-37867000	Weak transcription	NHLF	lung
25	chr2:37860800-37873000	Weak transcription	Pancreas	Pancrea
26	chr2:37860800-37879600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:37861000-37864600	Enhancers	Primary B cells from peripheral blood	blood
28	chr2:37861000-37865600	Enhancers	Fetal Thymus	thymus
29	chr2:37861000-37868000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:37861200-37864600	Enhancers	Primary T cells from cord blood	blood
31	chr2:37861800-37863600	Enhancers	HMEC	breast
32	chr2:37861800-37863600	Enhancers	NHEK	skin
33	chr2:37861800-37864200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:37861800-37864200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr2:37861800-37864200	Enhancers	Spleen	Spleen
36	chr2:37861800-37866200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:37862000-37864400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr2:37862000-37865600	Enhancers	Thymus	Thymus
39	chr2:37862000-37866600	Enhancers	HSMM	muscle
40	chr2:37862000-37867000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:37862000-37869400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:37862200-37863600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:37862200-37863600	Enhancers	Esophagus	oesophagus
44	chr2:37862200-37863600	Enhancers	Fetal Muscle Leg	muscle
45	chr2:37862200-37863600	Enhancers	NH-A	brain
46	chr2:37862200-37864400	Enhancers	Adipose Nuclei	Adipose
47	chr2:37862200-37865600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:37862200-37866800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:37862200-37867000	Enhancers	Muscle Satellite Cultured Cells	--
50	chr2:37862200-37867200	Enhancers	NHDF-Ad	bronchial

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