Variant report

Variant	rs4669706
Chromosome Location	chr2:11433497-11433498
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11433437..11435472-chr2:11482925..11485031,2	MCF-7	breast:
2	chr2:11432453..11434936-chr2:11435134..11437192,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10169455	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10175719	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10178332	0.90[AMR][1000 genomes]
rs10183296	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10192593	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10192994	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194620	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203916	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10206334	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10210600	0.84[AMR][1000 genomes]
rs10454126	0.86[AMR][1000 genomes]
rs10929729	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11681822	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694729	0.82[AMR][1000 genomes]
rs12477052	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12692434	0.86[AMR][1000 genomes]
rs12692435	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12992581	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12994807	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13002722	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13014721	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562748	0.86[AMR][1000 genomes]
rs1868584	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1901011	0.84[AMR][1000 genomes]
rs2060635	0.82[AMR][1000 genomes]
rs2084577	0.86[AMR][1000 genomes]
rs2122384	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2167126	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2230775	0.94[ASN][1000 genomes]
rs2290157	0.88[ASN][1000 genomes]
rs2357995	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3771109	0.94[ASN][1000 genomes]
rs4303693	0.90[AMR][1000 genomes]
rs4353615	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4668720	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4668721	0.81[AMR][1000 genomes]
rs4669699	0.81[AMR][1000 genomes]
rs4669701	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4669709	0.86[AMR][1000 genomes]
rs4669710	0.86[AMR][1000 genomes]
rs4669711	0.86[AMR][1000 genomes]
rs55714132	0.94[ASN][1000 genomes]
rs57082519	0.94[ASN][1000 genomes]
rs57282107	0.94[ASN][1000 genomes]
rs57339546	0.94[ASN][1000 genomes]
rs57861284	0.94[ASN][1000 genomes]
rs58007526	1.00[ASN][1000 genomes]
rs58275781	0.85[ASN][1000 genomes]
rs59194382	1.00[ASN][1000 genomes]
rs59211791	0.94[ASN][1000 genomes]
rs59266229	0.94[ASN][1000 genomes]
rs59883361	1.00[ASN][1000 genomes]
rs60643530	0.94[ASN][1000 genomes]
rs61575329	1.00[ASN][1000 genomes]
rs62118012	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6432184	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6432185	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6432186	0.86[AMR][1000 genomes]
rs6706126	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6710031	0.90[AMR][1000 genomes]
rs6713273	0.86[AMR][1000 genomes]
rs6713382	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6720821	1.00[ASN][1000 genomes]
rs6721445	0.84[AMR][1000 genomes]
rs6730673	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6732258	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6733312	0.86[AMR][1000 genomes]
rs6735090	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6736240	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6749456	0.86[AMR][1000 genomes]
rs6753875	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6755196	0.86[AMR][1000 genomes]
rs6755337	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6759490	0.94[ASN][1000 genomes]
rs72785499	0.94[ASN][1000 genomes]
rs7355446	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355489	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73915106	0.94[ASN][1000 genomes]
rs73915107	0.94[ASN][1000 genomes]
rs73915109	0.94[ASN][1000 genomes]
rs73915134	0.94[ASN][1000 genomes]
rs73915135	0.94[ASN][1000 genomes]
rs73915140	0.94[ASN][1000 genomes]
rs73915144	1.00[ASN][1000 genomes]
rs73915151	1.00[ASN][1000 genomes]
rs73915152	1.00[ASN][1000 genomes]
rs73915154	1.00[ASN][1000 genomes]
rs73915155	1.00[ASN][1000 genomes]
rs73915156	1.00[ASN][1000 genomes]
rs73915158	1.00[ASN][1000 genomes]
rs73915159	1.00[ASN][1000 genomes]
rs73915389	0.84[ASN][1000 genomes]
rs73915390	0.88[ASN][1000 genomes]
rs73915394	0.94[ASN][1000 genomes]
rs73915395	0.94[ASN][1000 genomes]
rs73915396	0.94[ASN][1000 genomes]
rs73917504	0.94[ASN][1000 genomes]
rs73917507	0.94[ASN][1000 genomes]
rs73917508	0.94[ASN][1000 genomes]
rs73917511	0.94[ASN][1000 genomes]
rs753770	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558664	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7563468	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7563928	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7568064	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7575837	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7586803	0.94[ASN][1000 genomes]
rs7593091	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7593966	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9712182	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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
rs4669706	PQLC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11424600-11436600	Weak transcription	Fetal Kidney	kidney
2	chr2:11424800-11455200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:11426000-11435800	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr2:11426000-11438200	Weak transcription	Ovary	ovary
5	chr2:11426000-11442400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:11426000-11444800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:11426200-11443400	Weak transcription	HSMM	muscle
8	chr2:11426400-11441600	Weak transcription	Fetal Intestine Small	intestine
9	chr2:11426600-11435800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:11426600-11442600	Weak transcription	Primary T cells from cord blood	blood
11	chr2:11426600-11446000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:11427200-11433600	Weak transcription	Primary B cells from cord blood	blood
13	chr2:11427200-11435600	Weak transcription	Fetal Intestine Large	intestine
14	chr2:11428800-11444200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:11429000-11439800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:11429000-11444800	Weak transcription	Left Ventricle	heart
17	chr2:11431600-11435000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:11431800-11433800	Enhancers	A549	lung
19	chr2:11431800-11434000	Enhancers	HUVEC	blood vessel
20	chr2:11432400-11433600	Enhancers	Liver	Liver
21	chr2:11432400-11433600	Enhancers	NHDF-Ad	bronchial
22	chr2:11432400-11433800	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr2:11432400-11434000	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr2:11432600-11433800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:11432600-11433800	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr2:11432800-11433600	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr2:11432800-11433600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:11432800-11433600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:11432800-11433600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:11432800-11433600	Enhancers	Right Ventricle	heart
31	chr2:11432800-11433800	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr2:11432800-11433800	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr2:11432800-11433800	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr2:11432800-11433800	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr2:11432800-11433800	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr2:11432800-11433800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr2:11432800-11433800	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr2:11432800-11433800	Enhancers	K562	blood
39	chr2:11432800-11434000	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr2:11432800-11434000	Enhancers	HepG2	liver
41	chr2:11433000-11433600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:11433000-11433600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:11433000-11433600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:11433000-11433600	Enhancers	Fetal Stomach	stomach
45	chr2:11433000-11433600	Enhancers	Stomach Mucosa	stomach
46	chr2:11433000-11433800	Enhancers	H1 Cell Line	embryonic stem cell
47	chr2:11433000-11433800	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr2:11433000-11433800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr2:11433000-11434000	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr2:11433000-11437600	Weak transcription	Fetal Heart	heart

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