Variant report

Variant	rs4669713
Chromosome Location	chr2:11478539-11478540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10173492	0.84[AMR][1000 genomes]
rs10178332	0.94[CEU][hapmap]
rs10192593	0.89[YRI][hapmap]
rs10192994	0.94[CEU][hapmap]
rs10194620	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs10203916	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs10205944	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs10210600	1.00[CEU][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes]
rs10454126	1.00[CEU][hapmap];0.97[YRI][hapmap]
rs10929732	0.81[YRI][hapmap];0.87[AMR][1000 genomes]
rs11694729	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11695377	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs12467103	0.84[AMR][1000 genomes]
rs12692434	1.00[CEU][hapmap];0.97[YRI][hapmap];0.84[AMR][1000 genomes]
rs12692435	0.84[YRI][hapmap]
rs12692437	1.00[CEU][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12990641	0.87[CEU][hapmap]
rs12992581	0.81[YRI][hapmap]
rs12994807	0.82[YRI][hapmap]
rs13015560	0.83[CEU][hapmap]
rs13016386	0.81[AMR][1000 genomes]
rs13017021	0.87[CEU][hapmap]
rs1562748	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs1562749	0.94[CEU][hapmap]
rs1868584	0.94[CEU][hapmap]
rs1901011	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2044758	0.94[CEU][hapmap]
rs2060635	0.80[AMR][1000 genomes]
rs2084577	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2122384	0.87[YRI][hapmap]
rs2357996	0.94[CEU][hapmap]
rs3911110	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs4303693	0.94[CEU][hapmap]
rs4668720	0.84[YRI][hapmap]
rs4668721	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4669709	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4669710	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4669711	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4669712	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4669715	0.93[CEU][hapmap]
rs62118012	0.84[AMR][1000 genomes]
rs6432183	0.94[CEU][hapmap]
rs6432184	0.94[CEU][hapmap]
rs6432186	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6706126	0.84[AMR][1000 genomes]
rs6710031	0.94[CEU][hapmap]
rs6713273	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs6721445	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs6730673	0.89[YRI][hapmap]
rs6733312	1.00[CEU][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes]
rs6735090	0.84[AMR][1000 genomes]
rs6736240	0.87[YRI][hapmap]
rs6749456	1.00[CEU][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6755196	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6755337	0.89[YRI][hapmap]
rs6760802	0.93[CEU][hapmap]
rs7355446	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs7355489	0.89[YRI][hapmap]
rs753770	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs7558664	0.89[YRI][hapmap]
rs7563468	0.93[YRI][hapmap]
rs7563928	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs7568064	0.84[YRI][hapmap]
rs7575837	0.84[YRI][hapmap]
rs7593091	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs9287728	0.94[CEU][hapmap]
rs965665	0.94[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526038	chr2:11369078-11489531	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4669713	PQLC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11467000-11480200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:11467400-11481200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:11467600-11481600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:11467800-11480200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:11468400-11481200	Weak transcription	HUVEC	blood vessel
6	chr2:11470400-11479800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:11470400-11481400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:11470800-11481200	Weak transcription	Right Atrium	heart
9	chr2:11470800-11481800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:11471000-11481200	Weak transcription	HSMM	muscle
11	chr2:11471200-11478600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:11471200-11480400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:11472200-11482800	Weak transcription	Gastric	stomach
14	chr2:11473600-11479800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:11473800-11479600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:11474000-11479800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:11474200-11480000	Weak transcription	Adipose Nuclei	Adipose
18	chr2:11475000-11481200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:11475400-11479800	Weak transcription	Aorta	Aorta
20	chr2:11475400-11481000	Weak transcription	Ovary	ovary
21	chr2:11475600-11478800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:11475800-11479200	Weak transcription	NHLF	lung
23	chr2:11475800-11479800	Weak transcription	Liver	Liver
24	chr2:11475800-11479800	Weak transcription	Stomach Mucosa	stomach
25	chr2:11475800-11481200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:11476000-11479800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:11476000-11479800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:11476000-11479800	Weak transcription	Osteobl	bone
29	chr2:11476000-11480000	Weak transcription	NHDF-Ad	bronchial
30	chr2:11476000-11480200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:11476200-11479200	Weak transcription	Hela-S3	cervix
32	chr2:11476200-11482200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr2:11476600-11482200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:11476600-11482800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:11476800-11479600	Weak transcription	Colon Smooth Muscle	Colon
36	chr2:11476800-11481000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:11476800-11481000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:11476800-11481200	Weak transcription	Psoas Muscle	Psoas
39	chr2:11476800-11482200	Weak transcription	Left Ventricle	heart
40	chr2:11476800-11482600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:11477000-11478600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:11477000-11480000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:11477200-11482200	Weak transcription	Fetal Stomach	stomach
44	chr2:11477400-11480200	Weak transcription	Fetal Intestine Large	intestine
45	chr2:11477800-11481000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:11478000-11478800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:11478000-11478800	Weak transcription	Fetal Muscle Leg	muscle
48	chr2:11478000-11479400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:11478200-11478800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:11478200-11479000	Genic enhancers	HepG2	liver

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