Variant report

Variant	rs13023677
Chromosome Location	chr2:11468326-11468327
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	chr2:11467535..11471011-chr2:11482918..11485202,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12472868	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12475627	0.80[ASN][1000 genomes]
rs12478870	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13022598	0.80[AFR][1000 genomes]
rs13030319	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2060634	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2122383	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2358007	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34193264	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34213264	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34586031	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34623763	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35407012	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35508648	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35515036	0.81[ASN][1000 genomes]
rs3771106	0.80[ASN][1000 genomes]
rs6707667	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs753771	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7557723	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7589152	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9677600	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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
rs13023677	PQLC3	cis	Esophagus Muscularis	GTEx
rs13023677	PQLC3	cis	Thyroid	GTEx
rs13023677	PQLC3	cis	lung	GTEx
rs13023677	ROCK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11454400-11469800	Weak transcription	Fetal Brain Male	brain
2	chr2:11455000-11469200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:11456000-11469400	Weak transcription	HSMM	muscle
4	chr2:11457200-11476400	Weak transcription	Fetal Intestine Small	intestine
5	chr2:11457400-11469800	Weak transcription	Hela-S3	cervix
6	chr2:11459800-11469400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:11460600-11469400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:11460800-11469800	Weak transcription	Fetal Lung	lung
9	chr2:11461000-11476400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:11461200-11469400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:11464400-11475200	Weak transcription	Aorta	Aorta
12	chr2:11466000-11468600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr2:11466200-11469400	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:11466600-11468400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:11466800-11468400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:11466800-11469000	Enhancers	HepG2	liver
17	chr2:11466800-11469600	Weak transcription	Liver	Liver
18	chr2:11467000-11468400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:11467000-11470200	Weak transcription	NHLF	lung
20	chr2:11467000-11480200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:11467400-11468400	Enhancers	HUVEC	blood vessel
22	chr2:11467400-11470000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:11467400-11470400	Weak transcription	K562	blood
24	chr2:11467400-11472600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr2:11467400-11481200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:11467600-11468400	Enhancers	Brain Germinal Matrix	brain
27	chr2:11467600-11468600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:11467600-11469400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:11467600-11469600	Weak transcription	A549	lung
30	chr2:11467600-11469600	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr2:11467600-11470400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr2:11467600-11471400	Weak transcription	Brain Angular Gyrus	brain
33	chr2:11467600-11472000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:11467600-11481600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:11467800-11469400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:11467800-11470000	Weak transcription	GM12878-XiMat	blood
37	chr2:11467800-11470400	Weak transcription	Right Atrium	heart
38	chr2:11467800-11470800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:11467800-11470800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:11467800-11471400	Weak transcription	Right Ventricle	heart
41	chr2:11467800-11471400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr2:11467800-11473400	Weak transcription	Adipose Nuclei	Adipose
43	chr2:11467800-11480200	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr2:11468000-11469800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:11468000-11470400	Weak transcription	Ovary	ovary
46	chr2:11468000-11476400	Weak transcription	Psoas Muscle	Psoas
47	chr2:11468200-11469200	Weak transcription	NHDF-Ad	bronchial
48	chr2:11468200-11470600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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