Variant report

Variant	rs10178332
Chromosome Location	chr2:11409017-11409018
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11407368..11409021-chr2:11484083..11485849,2	K562	blood:

Variant related genes	Relation type
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10168440	0.90[AFR][1000 genomes]
rs10169455	0.89[AMR][1000 genomes]
rs10175719	0.87[AMR][1000 genomes]
rs10183296	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10192593	0.83[AMR][1000 genomes]
rs10192994	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10194620	0.93[CEU][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10203916	0.94[CEU][hapmap];0.82[AMR][1000 genomes]
rs10205944	0.94[CEU][hapmap]
rs10206334	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10210600	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10454126	0.94[CEU][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10754957	0.94[EUR][1000 genomes]
rs10929730	0.82[EUR][1000 genomes]
rs11681822	0.82[AMR][1000 genomes]
rs11694729	0.94[CEU][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11695377	0.94[CEU][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12477052	0.81[AMR][1000 genomes]
rs12692434	0.94[CEU][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12692437	0.93[CEU][hapmap]
rs12990641	0.81[CEU][hapmap]
rs13002722	0.89[AMR][1000 genomes]
rs13017021	0.81[CEU][hapmap]
rs1515224	0.99[EUR][1000 genomes]
rs1562748	0.94[CEU][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1562749	0.89[CEU][hapmap];0.97[EUR][1000 genomes]
rs1868584	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs2044758	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2060635	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2084577	0.94[CEU][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2100228	0.94[EUR][1000 genomes]
rs2167126	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2357995	0.89[AMR][1000 genomes]
rs2357996	0.88[CEU][hapmap];0.97[EUR][1000 genomes]
rs3911110	0.94[CEU][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4303693	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4353615	0.87[AMR][1000 genomes]
rs4668720	0.85[AMR][1000 genomes]
rs4669699	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4669701	0.86[AMR][1000 genomes]
rs4669706	0.90[AMR][1000 genomes]
rs4669709	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4669710	0.94[CEU][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4669711	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4669713	0.94[CEU][hapmap]
rs4669715	0.87[CEU][hapmap]
rs62118012	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6432183	0.89[CEU][hapmap];0.97[EUR][1000 genomes]
rs6432184	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs6432186	0.94[CEU][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6706126	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6710031	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6713273	0.94[CEU][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6713382	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6721445	0.94[CEU][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6730673	0.83[AMR][1000 genomes]
rs6733312	0.94[CEU][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6735090	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6749456	0.94[CEU][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6753875	0.85[AMR][1000 genomes]
rs6755196	0.94[CEU][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6760802	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7355446	0.94[CEU][hapmap];0.82[AMR][1000 genomes]
rs753770	0.94[CEU][hapmap];0.82[AMR][1000 genomes]
rs7558664	0.87[AMR][1000 genomes]
rs7563468	0.85[AMR][1000 genomes]
rs7563928	0.94[CEU][hapmap];0.82[AMR][1000 genomes]
rs7568064	0.83[AMR][1000 genomes]
rs7573458	0.89[EUR][1000 genomes]
rs7593091	0.94[CEU][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7593966	0.80[AMR][1000 genomes]
rs9287728	0.89[CEU][hapmap];0.97[EUR][1000 genomes]
rs965665	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9808228	0.97[EUR][1000 genomes]
rs9967898	0.92[EUR][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	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	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
3	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
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10178332	PQLC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 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	chr2:11361000-11410800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:11361000-11411200	Weak transcription	Fetal Thymus	thymus
8	chr2:11361000-11416600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:11361200-11425600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:11364400-11423800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:11372600-11423800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:11376200-11410800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:11378800-11428600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:11382800-11410200	Weak transcription	Primary B cells from cord blood	blood
15	chr2:11383000-11424000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:11383200-11409800	Weak transcription	Primary T cells from cord blood	blood
17	chr2:11383400-11410400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr2:11385000-11411000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:11387800-11417400	Weak transcription	Placenta	Placenta
20	chr2:11388600-11411200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:11389600-11411000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:11389800-11410800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr2:11389800-11423800	Weak transcription	Colonic Mucosa	Colon
24	chr2:11391400-11410800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:11391400-11410800	Weak transcription	NHLF	lung
26	chr2:11391400-11411200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:11391400-11412600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:11391400-11423800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:11391400-11423800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:11391400-11423800	Weak transcription	Ovary	ovary
31	chr2:11391600-11411200	Weak transcription	Osteobl	bone
32	chr2:11391600-11414600	Weak transcription	HUVEC	blood vessel
33	chr2:11391600-11418000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:11391600-11424000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:11391600-11424000	Weak transcription	NHEK	skin
36	chr2:11392400-11423800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:11394600-11417600	Weak transcription	Fetal Lung	lung
38	chr2:11394800-11410600	Weak transcription	A549	lung
39	chr2:11394800-11411000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:11394800-11420400	Weak transcription	Small Intestine	intestine
41	chr2:11394800-11423800	Weak transcription	Fetal Kidney	kidney
42	chr2:11394800-11432800	Weak transcription	Right Ventricle	heart
43	chr2:11395400-11417400	Weak transcription	Brain Germinal Matrix	brain
44	chr2:11396400-11413200	Strong transcription	HepG2	liver
45	chr2:11396600-11423800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:11397600-11409200	Weak transcription	Fetal Intestine Small	intestine
47	chr2:11397600-11410400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:11397600-11412600	Weak transcription	Left Ventricle	heart
49	chr2:11397600-11412600	Weak transcription	Lung	lung
50	chr2:11397600-11414800	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links