Variant report

Variant	rs12478870
Chromosome Location	chr2:11459445-11459446
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	chr2:11459076..11460678-chr2:11484182..11486404,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10168084	0.81[EUR][1000 genomes]
rs10192483	0.81[EUR][1000 genomes]
rs10495582	0.80[EUR][1000 genomes]
rs10754958	0.87[AFR][1000 genomes]
rs11674991	0.81[EUR][1000 genomes]
rs12465116	0.80[EUR][1000 genomes]
rs12472868	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12475086	0.80[EUR][1000 genomes]
rs12478098	0.81[EUR][1000 genomes]
rs13022598	0.80[EUR][1000 genomes]
rs13023677	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13030319	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1515219	0.81[EUR][1000 genomes]
rs1546598	0.80[EUR][1000 genomes]
rs17366874	0.81[EUR][1000 genomes]
rs17463896	0.80[EUR][1000 genomes]
rs1901010	0.87[AFR][1000 genomes]
rs2060634	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2122383	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2357997	0.81[EUR][1000 genomes]
rs2358007	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34193264	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34213264	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34586031	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34623763	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35407012	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35508648	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35515036	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3771106	0.82[EUR][1000 genomes]
rs55641887	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs55995833	0.80[EUR][1000 genomes]
rs56256182	0.82[EUR][1000 genomes]
rs62121446	0.82[EUR][1000 genomes]
rs62121447	0.82[EUR][1000 genomes]
rs6707667	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6716447	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6728627	0.81[EUR][1000 genomes]
rs726843	0.80[EUR][1000 genomes]
rs753771	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7557723	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7560132	0.80[EUR][1000 genomes]
rs7589152	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9677600	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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
rs12478870	PQLC3	cis	Thyroid	GTEx
rs12478870	ROCK2	Cis_1M	lymphoblastoid	RTeQTL
rs12478870	PQLC3	cis	lung	GTEx
rs12478870	PQLC3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:38 , 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	chr2:11445400-11460200	Weak transcription	Left Ventricle	heart
3	chr2:11447000-11459800	Weak transcription	Fetal Kidney	kidney
4	chr2:11447000-11460000	Weak transcription	Ovary	ovary
5	chr2:11447000-11460200	Weak transcription	Fetal Lung	lung
6	chr2:11447200-11466200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:11448000-11465800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:11450600-11466600	Weak transcription	NHLF	lung
9	chr2:11451200-11460000	Weak transcription	Adipose Nuclei	Adipose
10	chr2:11451400-11461000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:11451600-11467000	Weak transcription	Primary B cells from cord blood	blood
12	chr2:11451800-11466000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:11452000-11460000	Weak transcription	Psoas Muscle	Psoas
14	chr2:11452000-11466000	Weak transcription	Small Intestine	intestine
15	chr2:11454400-11469800	Weak transcription	Fetal Brain Male	brain
16	chr2:11454600-11466000	Weak transcription	Brain Angular Gyrus	brain
17	chr2:11455000-11460000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:11455000-11460000	Weak transcription	K562	blood
19	chr2:11455000-11462800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:11455000-11469200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr2:11455200-11466600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:11455600-11465400	Weak transcription	NHDF-Ad	bronchial
23	chr2:11456000-11469400	Weak transcription	HSMM	muscle
24	chr2:11456200-11460000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:11456200-11460200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:11456200-11460200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:11456200-11460200	Weak transcription	Fetal Heart	heart
28	chr2:11456200-11466000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr2:11456800-11466400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:11457000-11460000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:11457200-11476400	Weak transcription	Fetal Intestine Small	intestine
32	chr2:11457400-11460200	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:11457400-11469800	Weak transcription	Hela-S3	cervix
34	chr2:11457600-11460200	Weak transcription	A549	lung
35	chr2:11457600-11460800	Weak transcription	Liver	Liver
36	chr2:11457600-11461000	Weak transcription	HepG2	liver
37	chr2:11459000-11460000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:11459400-11462800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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