Variant report

Variant	rs6753875
Chromosome Location	chr2:11434942-11434943
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	chr2:11433437..11435472-chr2:11482925..11485031,2	MCF-7	breast:
2	chr2:11434738..11436289-chr2:11444236..11445981,2	K562	blood:

Variant related genes	Relation type
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10169455	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10175719	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10178332	0.85[AMR][1000 genomes]
rs10183296	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10192994	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10194620	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10203916	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10206334	0.85[AMR][1000 genomes]
rs10454126	0.81[AMR][1000 genomes]
rs10929729	0.84[AFR][1000 genomes]
rs11681822	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12477052	0.80[AFR][1000 genomes]
rs12692434	0.81[AMR][1000 genomes]
rs12692435	0.89[AFR][1000 genomes]
rs12992581	0.84[AFR][1000 genomes]
rs12994807	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13002722	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs13014721	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1562748	0.81[AMR][1000 genomes]
rs1868584	0.84[EUR][1000 genomes]
rs2084577	0.81[AMR][1000 genomes]
rs2122384	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2167126	0.85[AMR][1000 genomes]
rs2357995	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4303693	0.85[AMR][1000 genomes]
rs4353615	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4668720	0.81[AMR][1000 genomes]
rs4669701	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4669706	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4669709	0.81[AMR][1000 genomes]
rs4669710	0.81[AMR][1000 genomes]
rs4669711	0.81[AMR][1000 genomes]
rs62118012	0.81[AMR][1000 genomes]
rs6432184	0.85[EUR][1000 genomes]
rs6432185	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6432186	0.81[AMR][1000 genomes]
rs6706126	0.89[AMR][1000 genomes]
rs6710031	0.85[AMR][1000 genomes]
rs6713273	0.81[AMR][1000 genomes]
rs6713382	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6732258	0.81[AMR][1000 genomes]
rs6733312	0.81[AMR][1000 genomes]
rs6735090	0.89[AMR][1000 genomes]
rs6736240	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6749456	0.81[AMR][1000 genomes]
rs6755196	0.81[AMR][1000 genomes]
rs6755337	0.82[AFR][1000 genomes]
rs7355446	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7355489	0.82[AFR][1000 genomes]
rs753770	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7558664	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7563468	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7563928	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7575837	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7593091	0.89[AMR][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
rs6753875	PQLC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

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	chr2:11427200-11435600	Weak transcription	Fetal Intestine Large	intestine
13	chr2:11428800-11444200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:11429000-11439800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:11429000-11444800	Weak transcription	Left Ventricle	heart
16	chr2:11431600-11435000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:11433000-11437600	Weak transcription	Fetal Heart	heart
18	chr2:11433200-11442600	Weak transcription	Psoas Muscle	Psoas
19	chr2:11433200-11445600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:11433200-11446200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:11433400-11443600	Weak transcription	Adipose Nuclei	Adipose
22	chr2:11433600-11435600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:11433600-11435800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:11433600-11436200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:11433600-11436800	Weak transcription	Stomach Mucosa	stomach
26	chr2:11433600-11439000	Weak transcription	Liver	Liver
27	chr2:11433600-11443400	Weak transcription	Colon Smooth Muscle	Colon
28	chr2:11433600-11444600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:11433600-11446800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:11433600-11448000	Weak transcription	Right Ventricle	heart
31	chr2:11433800-11435600	Weak transcription	K562	blood
32	chr2:11433800-11436200	Weak transcription	A549	lung
33	chr2:11433800-11437600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:11433800-11438800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:11434000-11438800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:11434000-11443400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr2:11434000-11443400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr2:11434600-11438800	Weak transcription	HepG2	liver

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