Variant report

Variant	rs7573458
Chromosome Location	chr2:11439107-11439108
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11436708..11439216-chr2:11441108..11443775,3	K562	blood:
2	chr2:11436411..11439216-chr2:11442275..11444665,2	K562	blood:
3	chr2:11437773..11439523-chr2:11445218..11447388,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10178332	0.89[EUR][1000 genomes]
rs10206334	0.92[EUR][1000 genomes]
rs10210600	0.92[EUR][1000 genomes]
rs10454126	0.89[EUR][1000 genomes]
rs10754957	0.89[EUR][1000 genomes]
rs10929730	0.89[EUR][1000 genomes]
rs11694729	0.89[EUR][1000 genomes]
rs12692434	0.94[EUR][1000 genomes]
rs1515224	0.90[EUR][1000 genomes]
rs1562748	0.92[EUR][1000 genomes]
rs1562749	0.92[EUR][1000 genomes]
rs2044758	0.88[EUR][1000 genomes]
rs2060635	0.88[EUR][1000 genomes]
rs2084577	0.92[EUR][1000 genomes]
rs2100228	0.94[EUR][1000 genomes]
rs2167126	0.92[EUR][1000 genomes]
rs2357996	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3911110	0.86[EUR][1000 genomes]
rs4303693	0.89[EUR][1000 genomes]
rs4669699	0.83[EUR][1000 genomes]
rs4669709	0.90[EUR][1000 genomes]
rs4669710	0.92[EUR][1000 genomes]
rs4669711	0.92[EUR][1000 genomes]
rs62118012	0.97[EUR][1000 genomes]
rs6432183	0.92[EUR][1000 genomes]
rs6432186	0.92[EUR][1000 genomes]
rs6706126	0.94[EUR][1000 genomes]
rs6710031	0.89[EUR][1000 genomes]
rs6713273	0.94[EUR][1000 genomes]
rs6721445	0.89[EUR][1000 genomes]
rs6733312	0.92[EUR][1000 genomes]
rs6735090	0.94[EUR][1000 genomes]
rs6749456	0.92[EUR][1000 genomes]
rs6755196	0.92[EUR][1000 genomes]
rs6760802	0.90[EUR][1000 genomes]
rs7593091	0.94[EUR][1000 genomes]
rs9287728	0.92[EUR][1000 genomes]
rs965665	0.90[EUR][1000 genomes]
rs9808228	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9967898	0.92[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	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	esv1827245	chr2:11385834-11442583	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	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
4	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
rs7573458	PQLC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11424800-11455200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:11426000-11442400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:11426000-11444800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:11426200-11443400	Weak transcription	HSMM	muscle
5	chr2:11426400-11441600	Weak transcription	Fetal Intestine Small	intestine
6	chr2:11426600-11442600	Weak transcription	Primary T cells from cord blood	blood
7	chr2:11426600-11446000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:11428800-11444200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:11429000-11439800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:11429000-11444800	Weak transcription	Left Ventricle	heart
11	chr2:11433200-11442600	Weak transcription	Psoas Muscle	Psoas
12	chr2:11433200-11445600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:11433200-11446200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:11433400-11443600	Weak transcription	Adipose Nuclei	Adipose
15	chr2:11433600-11443400	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:11433600-11444600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:11433600-11446800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:11433600-11448000	Weak transcription	Right Ventricle	heart
19	chr2:11434000-11443400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:11434000-11443400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:11437000-11443200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:11438000-11443200	Weak transcription	Fetal Heart	heart
23	chr2:11438400-11443000	Weak transcription	K562	blood
24	chr2:11438600-11441600	Weak transcription	Ovary	ovary
25	chr2:11438800-11439200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:11438800-11439200	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr2:11438800-11439600	Weak transcription	A549	lung
28	chr2:11438800-11440400	Enhancers	HepG2	liver
29	chr2:11439000-11440000	Enhancers	Liver	Liver

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