Variant report

Variant	rs2060634
Chromosome Location	chr2:11462926-11462927
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10192483	0.80[EUR][1000 genomes]
rs10754958	0.86[AFR][1000 genomes]
rs10929726	0.83[AFR][1000 genomes]
rs11674991	0.80[EUR][1000 genomes]
rs12465116	0.86[AFR][1000 genomes]
rs12470004	0.83[AFR][1000 genomes]
rs12472868	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12475627	0.82[ASN][1000 genomes]
rs12478870	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12996712	0.80[ASN][1000 genomes]
rs13023677	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13030319	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17366874	0.87[AFR][1000 genomes]
rs1901010	0.86[AFR][1000 genomes]
rs2122383	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2357997	0.80[EUR][1000 genomes]
rs2358007	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34193264	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34213264	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34586031	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34623763	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35407012	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35432367	0.84[AFR][1000 genomes]
rs35508648	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35515036	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3771106	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55641887	0.91[AFR][1000 genomes]
rs56256182	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57554471	0.83[AFR][1000 genomes]
rs62121446	0.81[EUR][1000 genomes]
rs62121447	0.81[EUR][1000 genomes]
rs6707667	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6716447	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6728627	0.80[EUR][1000 genomes]
rs753771	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7557723	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589152	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs921322	0.82[AFR][1000 genomes]
rs9677600	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2060634	PQLC3	cis	lung	GTEx
rs2060634	PQLC3	cis	Esophagus Muscularis	GTEx
rs2060634	PQLC3	cis	Thyroid	GTEx
rs2060634	ROCK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11445000-11465200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:11447200-11466200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:11448000-11465800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:11450600-11466600	Weak transcription	NHLF	lung
5	chr2:11451600-11467000	Weak transcription	Primary B cells from cord blood	blood
6	chr2:11451800-11466000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:11452000-11466000	Weak transcription	Small Intestine	intestine
8	chr2:11454400-11469800	Weak transcription	Fetal Brain Male	brain
9	chr2:11454600-11466000	Weak transcription	Brain Angular Gyrus	brain
10	chr2:11455000-11469200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:11455200-11466600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:11455600-11465400	Weak transcription	NHDF-Ad	bronchial
13	chr2:11456000-11469400	Weak transcription	HSMM	muscle
14	chr2:11456200-11466000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:11456800-11466400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:11457200-11476400	Weak transcription	Fetal Intestine Small	intestine
17	chr2:11457400-11469800	Weak transcription	Hela-S3	cervix
18	chr2:11459800-11469400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:11460000-11464200	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr2:11460600-11469400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:11460800-11469800	Weak transcription	Fetal Lung	lung
22	chr2:11461000-11463600	Weak transcription	A549	lung
23	chr2:11461000-11467200	Weak transcription	Right Ventricle	heart
24	chr2:11461000-11476400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:11461200-11463800	Weak transcription	Ovary	ovary
26	chr2:11461200-11465200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:11461200-11465400	Weak transcription	Brain Anterior Caudate	brain
28	chr2:11461200-11465400	Weak transcription	Colon Smooth Muscle	Colon
29	chr2:11461200-11466000	Weak transcription	Adipose Nuclei	Adipose
30	chr2:11461200-11466000	Weak transcription	Liver	Liver
31	chr2:11461200-11466000	Weak transcription	K562	blood
32	chr2:11461200-11469400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:11461400-11466000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:11461600-11465400	Weak transcription	Pancreas	Pancrea
35	chr2:11461600-11465400	Weak transcription	Right Atrium	heart
36	chr2:11462000-11463000	Enhancers	Fetal Heart	heart
37	chr2:11462000-11463400	Weak transcription	HepG2	liver
38	chr2:11462200-11463800	Weak transcription	Psoas Muscle	Psoas
39	chr2:11462200-11463800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:11462400-11465400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:11462400-11467600	Weak transcription	Left Ventricle	heart
42	chr2:11462800-11463000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:11462800-11463200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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