Variant report

Variant	rs62120156
Chromosome Location	chr2:11309920-11309921
allele	A/G
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	chr2:11309281-11309987	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:11309594-11309971	HUVEC	blood vessel:	n/a	n/a
3	CHD2	chr2:11309739-11309927	HepG2	liver:	n/a	n/a
4	TEAD4	chr2:11309401-11309975	HepG2	liver:	n/a	n/a
5	ELF1	chr2:11309340-11309921	HepG2	liver:	n/a	n/a
6	ZNF384	chr2:11309878-11309957	K562	blood:	n/a	n/a

Variant related genes	Relation type
PQLC3	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10168084	0.88[EUR][1000 genomes]
rs10176416	0.85[EUR][1000 genomes]
rs10192483	0.86[EUR][1000 genomes]
rs10495582	0.88[EUR][1000 genomes]
rs10929726	0.89[EUR][1000 genomes]
rs11674991	0.86[EUR][1000 genomes]
rs11680818	0.87[EUR][1000 genomes]
rs11691429	0.89[EUR][1000 genomes]
rs12465116	0.88[EUR][1000 genomes]
rs12470004	0.90[EUR][1000 genomes]
rs12472868	0.85[EUR][1000 genomes]
rs12475086	0.88[EUR][1000 genomes]
rs12478098	0.86[EUR][1000 genomes]
rs12987956	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12996399	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13013938	0.83[AMR][1000 genomes]
rs13018466	0.84[AMR][1000 genomes]
rs13022598	0.88[EUR][1000 genomes]
rs13424069	0.89[EUR][1000 genomes]
rs1515219	0.88[EUR][1000 genomes]
rs1546597	0.89[EUR][1000 genomes]
rs1546598	0.88[EUR][1000 genomes]
rs17366657	0.89[EUR][1000 genomes]
rs17366874	0.88[EUR][1000 genomes]
rs17463896	0.88[EUR][1000 genomes]
rs2176052	0.80[EUR][1000 genomes]
rs2357997	0.86[EUR][1000 genomes]
rs33985535	0.84[EUR][1000 genomes]
rs34213264	0.85[EUR][1000 genomes]
rs34727260	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35332442	0.81[EUR][1000 genomes]
rs35432367	0.87[EUR][1000 genomes]
rs35508648	0.84[EUR][1000 genomes]
rs35515036	0.84[EUR][1000 genomes]
rs35563401	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35898907	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3771106	0.87[EUR][1000 genomes]
rs3856468	0.83[AMR][1000 genomes]
rs3951242	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55641887	0.87[EUR][1000 genomes]
rs55995833	0.88[EUR][1000 genomes]
rs56256182	0.84[EUR][1000 genomes]
rs57554471	0.86[EUR][1000 genomes]
rs62120153	0.83[EUR][1000 genomes]
rs62120155	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs62121446	0.87[EUR][1000 genomes]
rs62121447	0.87[EUR][1000 genomes]
rs6711793	0.89[EUR][1000 genomes]
rs6716447	0.87[EUR][1000 genomes]
rs6728627	0.86[EUR][1000 genomes]
rs6753921	0.90[EUR][1000 genomes]
rs726843	0.88[EUR][1000 genomes]
rs7560132	0.87[EUR][1000 genomes]
rs7580593	0.89[EUR][1000 genomes]
rs7589152	0.84[EUR][1000 genomes]
rs7589629	0.87[EUR][1000 genomes]
rs8996	0.90[EUR][1000 genomes]
rs921322	0.91[EUR][1000 genomes]
rs978906	0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520789	chr2:11259067-11312224	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62120156	PQLC3	cis	Thyroid	GTEx
rs62120156	ROCK2	Cis_1M	lymphoblastoid	RTeQTL
rs62120156	PQLC3	cis	lung	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11296200-11329400	Weak transcription	Gastric	stomach
2	chr2:11296200-11412600	Weak transcription	Aorta	Aorta
3	chr2:11296400-11314200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:11296400-11314800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:11296400-11315200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:11296400-11315200	Weak transcription	Brain Substantia Nigra	brain
7	chr2:11296400-11315400	Weak transcription	Brain Angular Gyrus	brain
8	chr2:11296400-11318800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:11296600-11315200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:11296600-11315200	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:11296600-11315200	Weak transcription	NHDF-Ad	bronchial
12	chr2:11296600-11319200	Weak transcription	Fetal Lung	lung
13	chr2:11296800-11315000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr2:11296800-11315200	Weak transcription	Brain Anterior Caudate	brain
15	chr2:11296800-11318200	Weak transcription	A549	lung
16	chr2:11296800-11379800	Weak transcription	Small Intestine	intestine
17	chr2:11297600-11315200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:11297600-11394400	Weak transcription	Right Ventricle	heart
19	chr2:11297800-11315200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:11298200-11315400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:11298200-11317600	Weak transcription	Fetal Brain Male	brain
22	chr2:11299200-11357000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:11300200-11315400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:11300600-11315400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:11301400-11330400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:11301600-11315200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr2:11301800-11315400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr2:11301800-11324600	Weak transcription	Primary B cells from cord blood	blood
29	chr2:11302000-11315200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:11302400-11315200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr2:11302400-11315400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:11302400-11321400	Weak transcription	Fetal Intestine Small	intestine
33	chr2:11302400-11326200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr2:11302400-11335600	Weak transcription	Lung	lung
35	chr2:11303800-11314600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr2:11304200-11315200	Weak transcription	Primary T cells from cord blood	blood
37	chr2:11304200-11317800	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:11304400-11310200	Weak transcription	Spleen	Spleen
39	chr2:11304400-11314400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:11304400-11315200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:11304400-11315200	Weak transcription	HMEC	breast
42	chr2:11304400-11315200	Weak transcription	HSMM	muscle
43	chr2:11304400-11315400	Weak transcription	Left Ventricle	heart
44	chr2:11304400-11315400	Weak transcription	HSMMtube	muscle
45	chr2:11304400-11317800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:11304400-11321400	Weak transcription	Esophagus	oesophagus
47	chr2:11304400-11321400	Weak transcription	Fetal Stomach	stomach
48	chr2:11304400-11325200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr2:11304400-11326400	Weak transcription	Colon Smooth Muscle	Colon
50	chr2:11304400-11329200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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