Variant report

Variant	rs56256182
Chromosome Location	chr2:11412743-11412744
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11411018..11413119-chr2:11416854..11418915,2	K562	blood:
2	chr2:11410844..11413119-chr2:11416854..11418715,2	K562	blood:
3	chr2:11405281..11407608-chr2:11412695..11415283,2	K562	blood:

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10168084	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10169868	0.88[AMR][1000 genomes]
rs10176416	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10192483	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10495582	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10929725	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10929726	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11674991	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11680818	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11691429	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12465116	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12470004	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12472868	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12475086	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12475627	0.96[ASN][1000 genomes]
rs12478098	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12478870	0.82[EUR][1000 genomes]
rs12987956	0.86[EUR][1000 genomes]
rs12996399	0.82[EUR][1000 genomes]
rs12996712	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13022598	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13030319	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13393192	0.89[AMR][1000 genomes]
rs13397757	0.89[AMR][1000 genomes]
rs13404430	0.85[AMR][1000 genomes]
rs13423864	0.89[AMR][1000 genomes]
rs13424069	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1515219	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1546597	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1546598	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17366643	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17366657	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17366874	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17463896	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2011812	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2056103	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2060634	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2122383	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2176052	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2230774	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2357997	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2358007	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3206843	0.84[AMR][1000 genomes]
rs34193264	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34213264	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34586031	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34623763	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35407012	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35432367	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35508648	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35515036	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35563401	0.82[EUR][1000 genomes]
rs36072395	0.89[AMR][1000 genomes]
rs3771106	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4477886	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4595944	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs55641887	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55995833	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56243142	0.86[AMR][1000 genomes]
rs57554471	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58263533	0.85[AMR][1000 genomes]
rs62120156	0.84[EUR][1000 genomes]
rs62121446	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62121447	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6707667	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6711793	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6716447	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6716817	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6728627	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6753921	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs726843	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs753771	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7557723	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7560132	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7580593	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7581130	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7589152	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7589629	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7598032	0.89[AMR][1000 genomes]
rs7600696	0.89[AMR][1000 genomes]
rs8996	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs921321	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs921322	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs978906	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[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	esv3395022	chr2:11316915-11426380	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs56256182	PQLC3	cis	Thyroid	GTEx
rs56256182	PQLC3	cis	lung	GTEx
rs56256182	ROCK2	Cis_1M	lymphoblastoid	RTeQTL
rs56256182	PQLC3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11310600-11433000	Weak transcription	Pancreas	Pancrea
2	chr2:11352800-11424000	Weak transcription	HSMMtube	muscle
3	chr2:11354600-11423800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:11361000-11416600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr2:11361200-11425600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:11364400-11423800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:11372600-11423800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:11378800-11428600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:11383000-11424000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:11387800-11417400	Weak transcription	Placenta	Placenta
11	chr2:11389800-11423800	Weak transcription	Colonic Mucosa	Colon
12	chr2:11391400-11423800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:11391400-11423800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:11391400-11423800	Weak transcription	Ovary	ovary
15	chr2:11391600-11414600	Weak transcription	HUVEC	blood vessel
16	chr2:11391600-11418000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:11391600-11424000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:11391600-11424000	Weak transcription	NHEK	skin
19	chr2:11392400-11423800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr2:11394600-11417600	Weak transcription	Fetal Lung	lung
21	chr2:11394800-11420400	Weak transcription	Small Intestine	intestine
22	chr2:11394800-11423800	Weak transcription	Fetal Kidney	kidney
23	chr2:11394800-11432800	Weak transcription	Right Ventricle	heart
24	chr2:11395400-11417400	Weak transcription	Brain Germinal Matrix	brain
25	chr2:11396400-11413200	Strong transcription	HepG2	liver
26	chr2:11396600-11423800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:11397600-11414800	Weak transcription	GM12878-XiMat	blood
28	chr2:11397600-11417400	Weak transcription	Adipose Nuclei	Adipose
29	chr2:11397600-11423200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:11397800-11417600	Weak transcription	Liver	Liver
31	chr2:11397800-11417800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:11403600-11413600	Weak transcription	K562	blood
33	chr2:11404400-11423800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:11404400-11423800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:11404600-11423800	Weak transcription	Colon Smooth Muscle	Colon
36	chr2:11404800-11423800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr2:11404800-11423800	Weak transcription	Fetal Heart	heart
38	chr2:11406200-11423800	Weak transcription	Fetal Brain Female	brain
39	chr2:11408200-11412800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:11408600-11418000	Weak transcription	Hela-S3	cervix
41	chr2:11409000-11417400	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr2:11409000-11424000	Weak transcription	Fetal Brain Male	brain
43	chr2:11409400-11423800	Weak transcription	NH-A	brain
44	chr2:11409600-11413400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:11409800-11423800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:11409800-11424200	Weak transcription	HMEC	breast
47	chr2:11410200-11423000	Weak transcription	Fetal Intestine Small	intestine
48	chr2:11410400-11433000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr2:11410800-11415400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr2:11410800-11432800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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