Variant report

Variant	rs58263533
Chromosome Location	chr2:11329053-11329054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11325707..11330168-chr2:11330968..11335398,4	MCF-7	breast:
2	chr2:11327523..11329314-chr2:11335510..11337829,2	K562	blood:

Variant related genes	Relation type
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10167277	0.92[ASN][1000 genomes]
rs10168084	0.88[AMR][1000 genomes]
rs10169868	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10176416	0.87[AMR][1000 genomes]
rs10180914	0.84[ASN][1000 genomes]
rs10181567	0.97[ASN][1000 genomes]
rs10187981	0.97[ASN][1000 genomes]
rs10192483	0.83[AMR][1000 genomes]
rs10204503	0.89[ASN][1000 genomes]
rs10495582	0.88[AMR][1000 genomes]
rs10929725	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10929726	0.88[AMR][1000 genomes]
rs10929727	0.95[ASN][1000 genomes]
rs10929728	0.90[ASN][1000 genomes]
rs1129976	0.97[ASN][1000 genomes]
rs11674991	0.83[AMR][1000 genomes]
rs11676201	0.91[ASN][1000 genomes]
rs11680818	0.82[AMR][1000 genomes]
rs11683010	0.91[ASN][1000 genomes]
rs11691429	0.88[AMR][1000 genomes]
rs11891877	0.99[ASN][1000 genomes]
rs12465116	0.86[AMR][1000 genomes]
rs12469980	0.86[ASN][1000 genomes]
rs12470004	0.88[AMR][1000 genomes]
rs12472868	0.85[AMR][1000 genomes]
rs12475086	0.89[AMR][1000 genomes]
rs12476188	0.82[ASN][1000 genomes]
rs12478098	0.83[AMR][1000 genomes]
rs12618325	0.92[ASN][1000 genomes]
rs12996399	0.82[ASN][1000 genomes]
rs13013938	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13017010	0.92[ASN][1000 genomes]
rs13018466	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13022598	0.84[AMR][1000 genomes]
rs13393192	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13397757	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13404430	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13423864	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13424069	0.88[AMR][1000 genomes]
rs1515219	0.83[AMR][1000 genomes]
rs1546597	0.88[AMR][1000 genomes]
rs1546598	0.89[AMR][1000 genomes]
rs17366643	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17366657	0.85[AMR][1000 genomes]
rs17366874	0.86[AMR][1000 genomes]
rs17463896	0.85[AMR][1000 genomes]
rs1868585	0.97[ASN][1000 genomes]
rs2011812	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2056103	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2176052	0.81[AMR][1000 genomes]
rs2230774	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2271621	0.95[ASN][1000 genomes]
rs2290156	0.98[ASN][1000 genomes]
rs2357997	0.83[AMR][1000 genomes]
rs3206843	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34213264	0.85[AMR][1000 genomes]
rs34554628	0.90[ASN][1000 genomes]
rs35432367	0.86[AMR][1000 genomes]
rs35508648	0.86[AMR][1000 genomes]
rs35515036	0.86[AMR][1000 genomes]
rs36072395	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3732103	0.81[ASN][1000 genomes]
rs3771106	0.84[AMR][1000 genomes]
rs4595944	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4669700	0.93[ASN][1000 genomes]
rs4669702	0.92[ASN][1000 genomes]
rs55641887	0.86[AMR][1000 genomes]
rs55995833	0.85[AMR][1000 genomes]
rs56243142	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56256182	0.85[AMR][1000 genomes]
rs57554471	0.86[AMR][1000 genomes]
rs62121446	0.85[AMR][1000 genomes]
rs62121447	0.85[AMR][1000 genomes]
rs6711793	0.90[AMR][1000 genomes]
rs6716447	0.84[AMR][1000 genomes]
rs6728627	0.83[AMR][1000 genomes]
rs6753921	0.92[AMR][1000 genomes]
rs726843	0.85[AMR][1000 genomes]
rs7560132	0.83[AMR][1000 genomes]
rs7580593	0.88[AMR][1000 genomes]
rs7581130	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7589152	0.86[AMR][1000 genomes]
rs7589629	0.82[AMR][1000 genomes]
rs7598032	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7600696	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8996	0.90[AMR][1000 genomes]
rs921321	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs921322	0.88[AMR][1000 genomes]
rs978906	0.90[AMR][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	nsv1012083	chr2:11316299-11350604	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
2	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
3	nsv1013570	chr2:11321519-11405246	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs58263533	PQLC3	cis	Esophagus Muscularis	GTEx
rs58263533	ROCK2	Cis_1M	lymphoblastoid	RTeQTL
rs58263533	PQLC3	cis	Thyroid	GTEx
rs58263533	PQLC3	cis	lung	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

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	chr2:11296800-11379800	Weak transcription	Small Intestine	intestine
4	chr2:11297600-11394400	Weak transcription	Right Ventricle	heart
5	chr2:11299200-11357000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:11301400-11330400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:11302400-11335600	Weak transcription	Lung	lung
8	chr2:11304400-11329200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:11309800-11335600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:11310000-11337200	Weak transcription	Ovary	ovary
11	chr2:11310600-11433000	Weak transcription	Pancreas	Pancrea
12	chr2:11314600-11329600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:11314600-11332200	Weak transcription	Colonic Mucosa	Colon
14	chr2:11314600-11364200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:11315800-11329200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr2:11315800-11335200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:11315800-11336200	Weak transcription	Brain Anterior Caudate	brain
18	chr2:11315800-11336400	Weak transcription	GM12878-XiMat	blood
19	chr2:11315800-11336600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:11315800-11339000	Weak transcription	Spleen	Spleen
21	chr2:11315800-11340400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:11315800-11367400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:11316000-11331200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:11316000-11332200	Weak transcription	Psoas Muscle	Psoas
25	chr2:11316000-11338000	Weak transcription	Brain Substantia Nigra	brain
26	chr2:11316200-11331200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:11316200-11332600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:11316200-11333000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr2:11316200-11336200	Weak transcription	Thymus	Thymus
30	chr2:11316200-11344400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:11316200-11354200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr2:11316400-11351800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:11316600-11339000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:11317800-11332200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr2:11317800-11333000	Weak transcription	Fetal Brain Male	brain
36	chr2:11318400-11332600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr2:11318600-11330600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:11318600-11336200	Weak transcription	Brain Angular Gyrus	brain
39	chr2:11318600-11359200	Weak transcription	Fetal Heart	heart
40	chr2:11319000-11364200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:11319400-11332600	Weak transcription	Brain Germinal Matrix	brain
42	chr2:11319400-11334000	Strong transcription	Fetal Intestine Large	intestine
43	chr2:11320800-11377000	Strong transcription	HepG2	liver
44	chr2:11321000-11329200	Weak transcription	Fetal Brain Female	brain
45	chr2:11321000-11331200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:11321000-11332600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:11321800-11330400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr2:11323000-11329200	Weak transcription	Brain Hippocampus Middle	brain
49	chr2:11323000-11329400	Weak transcription	Fetal Lung	lung
50	chr2:11323600-11329200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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