Variant report

Variant	rs12692434
Chromosome Location	chr2:11442583-11442584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11436411..11439216-chr2:11442275..11444665,2	K562	blood:
2	chr2:11436708..11439216-chr2:11441108..11443775,3	K562	blood:
3	chr2:11428310..11431014-chr2:11439661..11442646,2	MCF-7	breast:
4	chr2:11431258..11433262-chr2:11441914..11443504,2	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10168440	0.85[AFR][1000 genomes]
rs10178332	0.94[CEU][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10183296	0.82[AMR][1000 genomes]
rs10192593	0.86[YRI][hapmap]
rs10192994	0.94[CEU][hapmap];0.82[AMR][1000 genomes]
rs10194620	1.00[CEU][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes]
rs10203916	1.00[CEU][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10205944	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs10206334	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10210600	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10454126	1.00[CEU][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10754957	0.84[EUR][1000 genomes]
rs10929730	0.92[EUR][1000 genomes]
rs10929732	0.84[YRI][hapmap]
rs11681822	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11694729	1.00[CEU][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11695377	1.00[CEU][hapmap];0.97[YRI][hapmap];0.85[AFR][1000 genomes]
rs12692435	0.88[YRI][hapmap];0.83[AMR][1000 genomes]
rs12692437	1.00[CEU][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes]
rs12990641	0.86[CEU][hapmap]
rs12992581	0.84[YRI][hapmap];0.87[AMR][1000 genomes]
rs12994807	0.89[AMR][1000 genomes]
rs13014721	0.90[AMR][1000 genomes]
rs13015560	0.82[CEU][hapmap]
rs13017021	0.86[CEU][hapmap]
rs1515224	0.88[EUR][1000 genomes]
rs1562748	1.00[CEU][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1562749	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs1868584	0.94[CEU][hapmap]
rs2044758	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs2060635	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2084577	1.00[CEU][hapmap];0.97[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2100228	0.89[EUR][1000 genomes]
rs2122384	0.84[YRI][hapmap];0.89[AMR][1000 genomes]
rs2167126	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2357996	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs3911110	1.00[CEU][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes]
rs4303693	0.94[CEU][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4668720	0.81[YRI][hapmap]
rs4669699	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4669706	0.86[AMR][1000 genomes]
rs4669709	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4669710	1.00[CEU][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4669711	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4669712	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4669713	1.00[CEU][hapmap];0.97[YRI][hapmap];0.84[AMR][1000 genomes]
rs4669715	0.93[CEU][hapmap]
rs62118012	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6432183	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs6432184	0.94[CEU][hapmap]
rs6432185	0.89[AMR][1000 genomes]
rs6432186	1.00[CEU][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6706126	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6710031	0.94[CEU][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6713273	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6713382	0.82[AMR][1000 genomes]
rs6721445	1.00[CEU][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6730673	0.86[YRI][hapmap]
rs6733312	1.00[CEU][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6735090	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6736240	0.84[YRI][hapmap];0.89[AMR][1000 genomes]
rs6749456	1.00[CEU][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6753875	0.81[AMR][1000 genomes]
rs6755196	1.00[CEU][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6755337	0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs6760802	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs7355446	1.00[CEU][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes]
rs7355489	0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs753770	1.00[CEU][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes]
rs7558664	0.86[YRI][hapmap]
rs7563468	0.96[YRI][hapmap];0.81[AMR][1000 genomes]
rs7563928	1.00[CEU][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7568064	0.81[YRI][hapmap]
rs7573458	0.94[EUR][1000 genomes]
rs7575837	0.88[YRI][hapmap];0.89[AMR][1000 genomes]
rs7593091	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9287728	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs965665	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs9712182	0.89[AMR][1000 genomes]
rs9808228	0.86[EUR][1000 genomes]
rs9967898	0.87[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	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
rs12692434	PQLC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11424800-11455200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:11426000-11444800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:11426200-11443400	Weak transcription	HSMM	muscle
4	chr2:11426600-11442600	Weak transcription	Primary T cells from cord blood	blood
5	chr2:11426600-11446000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:11428800-11444200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:11429000-11444800	Weak transcription	Left Ventricle	heart
8	chr2:11433200-11442600	Weak transcription	Psoas Muscle	Psoas
9	chr2:11433200-11445600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:11433200-11446200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:11433400-11443600	Weak transcription	Adipose Nuclei	Adipose
12	chr2:11433600-11443400	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:11433600-11444600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:11433600-11446800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:11433600-11448000	Weak transcription	Right Ventricle	heart
16	chr2:11434000-11443400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:11434000-11443400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:11437000-11443200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:11438000-11443200	Weak transcription	Fetal Heart	heart
20	chr2:11438400-11443000	Weak transcription	K562	blood
21	chr2:11439200-11443400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:11439200-11453000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:11440000-11445800	Weak transcription	Liver	Liver
24	chr2:11440200-11446000	Weak transcription	A549	lung
25	chr2:11440400-11444000	Weak transcription	HepG2	liver
26	chr2:11441000-11445800	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr2:11441600-11442600	ZNF genes & repeats	Fetal Intestine Small	intestine
28	chr2:11442200-11443400	Weak transcription	Ovary	ovary
29	chr2:11442200-11446000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr2:11442400-11442800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:11442400-11443200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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