Variant report

Variant	rs6432183
Chromosome Location	chr2:11399492-11399493
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	chr2:11394019..11396921-chr2:11397879..11400612,3	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10178332	0.89[CEU][hapmap];0.97[EUR][1000 genomes]
rs10183296	0.80[EUR][1000 genomes]
rs10192994	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs10194620	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs10203916	0.93[CEU][hapmap]
rs10205944	0.93[CEU][hapmap]
rs10206334	0.94[EUR][1000 genomes]
rs10210600	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs10454126	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs10754957	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10929730	0.81[EUR][1000 genomes]
rs11694729	0.93[CEU][hapmap];0.97[EUR][1000 genomes]
rs11695377	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs12692434	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs12692437	0.93[CEU][hapmap]
rs12990641	0.93[CEU][hapmap]
rs13015560	0.88[CEU][hapmap]
rs13017021	0.93[CEU][hapmap]
rs1515224	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1562748	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs1562749	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1868584	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2044758	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2060635	0.80[EUR][1000 genomes]
rs2084577	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs2100228	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2167126	0.94[EUR][1000 genomes]
rs2357996	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3911110	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs4303693	0.89[CEU][hapmap];0.97[EUR][1000 genomes]
rs4669699	0.91[EUR][1000 genomes]
rs4669709	0.83[EUR][1000 genomes]
rs4669710	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs4669711	0.84[EUR][1000 genomes]
rs4669713	0.94[CEU][hapmap]
rs4669715	1.00[CEU][hapmap]
rs62118012	0.89[EUR][1000 genomes]
rs6432184	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6432186	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs6706126	0.92[EUR][1000 genomes]
rs6710031	0.88[CEU][hapmap];0.97[EUR][1000 genomes]
rs6713273	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs6713382	0.80[EUR][1000 genomes]
rs6721445	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs6733312	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs6735090	0.92[EUR][1000 genomes]
rs6749456	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs6755196	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs6760802	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7355446	0.94[CEU][hapmap]
rs753770	0.93[CEU][hapmap]
rs7563928	0.94[CEU][hapmap]
rs7573458	0.92[EUR][1000 genomes]
rs7593091	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs9287728	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs965665	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9808228	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9967898	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1013570	chr2:11321519-11405246	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	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
4	nsv2607	chr2:11381341-11409932	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	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
6	nsv436304	chr2:11394989-11401393	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv16727	chr2:11395030-11400620	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv498912	chr2:11395188-11400430	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv514052	chr2:11395366-11400290	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6432183	PQLC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11296200-11412600	Weak transcription	Aorta	Aorta
2	chr2:11310600-11433000	Weak transcription	Pancreas	Pancrea
3	chr2:11352600-11411200	Weak transcription	Thymus	Thymus
4	chr2:11352800-11424000	Weak transcription	HSMMtube	muscle
5	chr2:11354600-11423800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:11361000-11400200	Weak transcription	Gastric	stomach
7	chr2:11361000-11410800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:11361000-11411200	Weak transcription	Fetal Thymus	thymus
9	chr2:11361000-11416600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:11361200-11425600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:11364400-11423800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:11372600-11423800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:11376200-11410800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:11378800-11428600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:11382800-11410200	Weak transcription	Primary B cells from cord blood	blood
16	chr2:11383000-11424000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:11383200-11409800	Weak transcription	Primary T cells from cord blood	blood
18	chr2:11383400-11410400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:11385000-11411000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:11387800-11417400	Weak transcription	Placenta	Placenta
21	chr2:11388400-11401000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:11388600-11406400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr2:11388600-11411200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr2:11389600-11411000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:11389800-11410800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:11389800-11423800	Weak transcription	Colonic Mucosa	Colon
27	chr2:11391200-11403400	Weak transcription	K562	blood
28	chr2:11391400-11400600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:11391400-11410800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:11391400-11410800	Weak transcription	NHLF	lung
31	chr2:11391400-11411200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:11391400-11412600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr2:11391400-11423800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:11391400-11423800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr2:11391400-11423800	Weak transcription	Ovary	ovary
36	chr2:11391600-11404800	Weak transcription	NHDF-Ad	bronchial
37	chr2:11391600-11411200	Weak transcription	Osteobl	bone
38	chr2:11391600-11414600	Weak transcription	HUVEC	blood vessel
39	chr2:11391600-11418000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr2:11391600-11424000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:11391600-11424000	Weak transcription	NHEK	skin
42	chr2:11392400-11423800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr2:11394600-11403200	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:11394600-11417600	Weak transcription	Fetal Lung	lung
45	chr2:11394800-11403200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr2:11394800-11403600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr2:11394800-11410600	Weak transcription	A549	lung
48	chr2:11394800-11411000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:11394800-11420400	Weak transcription	Small Intestine	intestine
50	chr2:11394800-11423800	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links