Variant report

Variant	rs10754957
Chromosome Location	chr2:11319253-11319254
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11318764..11322835-chr2:11322965..11327075,5	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10178332	0.94[EUR][1000 genomes]
rs10206334	0.92[EUR][1000 genomes]
rs10210600	0.81[EUR][1000 genomes]
rs10454126	0.94[EUR][1000 genomes]
rs11694729	0.94[EUR][1000 genomes]
rs12692434	0.84[EUR][1000 genomes]
rs1515224	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1562748	0.81[EUR][1000 genomes]
rs1562749	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2044758	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2084577	0.81[EUR][1000 genomes]
rs2100228	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2167126	0.92[EUR][1000 genomes]
rs2357996	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3911110	0.97[EUR][1000 genomes]
rs4303693	0.94[EUR][1000 genomes]
rs4669699	0.88[EUR][1000 genomes]
rs4669709	0.80[EUR][1000 genomes]
rs4669710	0.81[EUR][1000 genomes]
rs4669711	0.81[EUR][1000 genomes]
rs62118012	0.86[EUR][1000 genomes]
rs6432183	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6432186	0.81[EUR][1000 genomes]
rs6706126	0.89[EUR][1000 genomes]
rs6710031	0.94[EUR][1000 genomes]
rs6713273	0.84[EUR][1000 genomes]
rs6721445	0.94[EUR][1000 genomes]
rs6733312	0.81[EUR][1000 genomes]
rs6735090	0.89[EUR][1000 genomes]
rs6749456	0.81[EUR][1000 genomes]
rs6755196	0.81[EUR][1000 genomes]
rs6760802	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73175657	0.91[AFR][1000 genomes]
rs7573458	0.89[EUR][1000 genomes]
rs7593091	0.89[EUR][1000 genomes]
rs9287728	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs965665	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9808228	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9967898	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012083	chr2:11316299-11350604	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
2	esv3395022	chr2:11316915-11426380	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10754957	PQLC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11296200-11329400	Weak transcription	Gastric	stomach
2	chr2:11296200-11412600	Weak transcription	Aorta	Aorta
3	chr2:11296800-11379800	Weak transcription	Small Intestine	intestine
4	chr2:11297600-11394400	Weak transcription	Right Ventricle	heart
5	chr2:11299200-11357000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:11301400-11330400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:11301800-11324600	Weak transcription	Primary B cells from cord blood	blood
8	chr2:11302400-11321400	Weak transcription	Fetal Intestine Small	intestine
9	chr2:11302400-11326200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:11302400-11335600	Weak transcription	Lung	lung
11	chr2:11304400-11321400	Weak transcription	Esophagus	oesophagus
12	chr2:11304400-11321400	Weak transcription	Fetal Stomach	stomach
13	chr2:11304400-11325200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:11304400-11326400	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:11304400-11329200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:11309800-11327200	Weak transcription	K562	blood
17	chr2:11309800-11335600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:11310000-11337200	Weak transcription	Ovary	ovary
19	chr2:11310600-11433000	Weak transcription	Pancreas	Pancrea
20	chr2:11312800-11319400	Weak transcription	Fetal Intestine Large	intestine
21	chr2:11314600-11329600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr2:11314600-11332200	Weak transcription	Colonic Mucosa	Colon
23	chr2:11314600-11364200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:11314800-11321400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:11315600-11319400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:11315600-11321600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr2:11315800-11320000	Weak transcription	Left Ventricle	heart
28	chr2:11315800-11321800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:11315800-11322000	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:11315800-11322800	Weak transcription	Fetal Thymus	thymus
31	chr2:11315800-11326400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr2:11315800-11327400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:11315800-11329200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr2:11315800-11335200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:11315800-11336200	Weak transcription	Brain Anterior Caudate	brain
36	chr2:11315800-11336400	Weak transcription	GM12878-XiMat	blood
37	chr2:11315800-11336600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr2:11315800-11339000	Weak transcription	Spleen	Spleen
39	chr2:11315800-11340400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:11315800-11367400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr2:11316000-11326400	Weak transcription	HSMMtube	muscle
42	chr2:11316000-11331200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:11316000-11332200	Weak transcription	Psoas Muscle	Psoas
44	chr2:11316000-11338000	Weak transcription	Brain Substantia Nigra	brain
45	chr2:11316200-11319400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:11316200-11320000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:11316200-11320800	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:11316200-11321600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:11316200-11325200	Weak transcription	HUVEC	blood vessel
50	chr2:11316200-11329000	Weak transcription	NHEK	skin

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