Variant report

Variant	rs4669711
Chromosome Location	chr2:11467770-11467771
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	chr2:11465940..11468205-chr2:11479384..11482432,3	MCF-7	breast:
2	chr2:11467535..11471011-chr2:11482918..11485202,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10168440	0.84[AFR][1000 genomes]
rs10178332	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10183296	0.82[AMR][1000 genomes]
rs10192994	0.82[AMR][1000 genomes]
rs10194620	0.82[AMR][1000 genomes]
rs10203916	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10206334	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10210600	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10454126	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10754957	0.81[EUR][1000 genomes]
rs10929730	0.95[EUR][1000 genomes]
rs11681822	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11694729	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11695377	0.84[AFR][1000 genomes]
rs12692434	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12692435	0.83[AMR][1000 genomes]
rs12692437	0.84[AMR][1000 genomes]
rs12992581	0.87[AMR][1000 genomes]
rs12994807	0.89[AMR][1000 genomes]
rs13014721	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1515224	0.85[EUR][1000 genomes]
rs1562748	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1562749	0.84[EUR][1000 genomes]
rs2044758	0.85[EUR][1000 genomes]
rs2060635	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2084577	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2100228	0.86[EUR][1000 genomes]
rs2122384	0.89[AMR][1000 genomes]
rs2167126	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2357996	0.84[EUR][1000 genomes]
rs3911110	0.84[EUR][1000 genomes]
rs4303693	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4669699	0.81[EUR][1000 genomes]
rs4669706	0.86[AMR][1000 genomes]
rs4669709	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4669710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4669712	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4669713	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62118012	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6432183	0.84[EUR][1000 genomes]
rs6432185	0.89[AMR][1000 genomes]
rs6432186	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6706126	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6710031	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6713273	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6713382	0.82[AMR][1000 genomes]
rs6721445	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6733312	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6735090	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6736240	0.89[AMR][1000 genomes]
rs6749456	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6753875	0.81[AMR][1000 genomes]
rs6755196	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6755337	0.87[AMR][1000 genomes]
rs6760802	0.85[EUR][1000 genomes]
rs7355446	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7355489	0.87[AMR][1000 genomes]
rs753770	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7563468	0.81[AMR][1000 genomes]
rs7563928	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7573458	0.92[EUR][1000 genomes]
rs7575837	0.89[AMR][1000 genomes]
rs7593091	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9287728	0.84[EUR][1000 genomes]
rs965665	0.85[EUR][1000 genomes]
rs9712182	0.89[AMR][1000 genomes]
rs9808228	0.84[EUR][1000 genomes]
rs9967898	0.84[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4669711	PQLC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

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	chr2:11465200-11467800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:11465400-11467800	Enhancers	Brain Anterior Caudate	brain
14	chr2:11466000-11467800	Enhancers	Adipose Nuclei	Adipose
15	chr2:11466000-11467800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr2:11466000-11468600	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr2:11466200-11469400	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:11466400-11467800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr2:11466400-11468000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:11466600-11467800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:11466600-11467800	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr2:11466600-11467800	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr2:11466600-11468000	Enhancers	Psoas Muscle	Psoas
24	chr2:11466600-11468400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:11466800-11468400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:11466800-11469000	Enhancers	HepG2	liver
27	chr2:11466800-11469600	Weak transcription	Liver	Liver
28	chr2:11467000-11467800	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr2:11467000-11467800	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr2:11467000-11467800	Enhancers	GM12878-XiMat	blood
31	chr2:11467000-11468200	Enhancers	NHDF-Ad	bronchial
32	chr2:11467000-11468400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:11467000-11470200	Weak transcription	NHLF	lung
34	chr2:11467000-11480200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:11467200-11467800	Enhancers	Right Ventricle	heart
36	chr2:11467200-11468000	Enhancers	Ovary	ovary
37	chr2:11467200-11468200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:11467200-11468200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:11467400-11467800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:11467400-11468200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr2:11467400-11468400	Enhancers	HUVEC	blood vessel
42	chr2:11467400-11470000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:11467400-11470400	Weak transcription	K562	blood
44	chr2:11467400-11472600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:11467400-11481200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:11467600-11467800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:11467600-11467800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:11467600-11467800	Enhancers	Right Atrium	heart
49	chr2:11467600-11468000	Enhancers	Left Ventricle	heart
50	chr2:11467600-11468400	Enhancers	Brain Germinal Matrix	brain

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