Variant report

Variant	rs4669710
Chromosome Location	chr2:11466513-11466514
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11465940..11468205-chr2:11479384..11482432,3	MCF-7	breast:
2	chr2:11465949..11467499-chr2:11475511..11477428,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10168440	0.84[AFR][1000 genomes]
rs10178332	0.94[CEU][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10183296	0.82[AMR][1000 genomes]
rs10192593	0.90[YRI][hapmap]
rs10192994	0.94[CEU][hapmap];0.82[AMR][1000 genomes]
rs10194620	1.00[CEU][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes]
rs10203916	1.00[CEU][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10205944	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs10206334	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10210600	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10454126	1.00[CEU][hapmap];0.97[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10754957	0.81[EUR][1000 genomes]
rs10929730	0.95[EUR][1000 genomes]
rs10929732	0.81[YRI][hapmap]
rs11681822	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11694729	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11695377	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs12692434	1.00[CEU][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12692435	0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs12692437	1.00[CEU][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes]
rs12990641	0.87[CEU][hapmap]
rs12992581	0.81[YRI][hapmap];0.87[AMR][1000 genomes]
rs12994807	0.82[YRI][hapmap];0.89[AMR][1000 genomes]
rs13014721	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13015560	0.83[CEU][hapmap]
rs13017021	0.87[CEU][hapmap]
rs1515224	0.85[EUR][1000 genomes]
rs1562748	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1562749	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs1868584	0.94[CEU][hapmap]
rs2044758	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs2060635	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2084577	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2100228	0.86[EUR][1000 genomes]
rs2122384	0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs2167126	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2357996	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs3911110	1.00[CEU][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes]
rs4303693	0.94[CEU][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4668720	0.85[YRI][hapmap]
rs4669699	0.81[EUR][1000 genomes]
rs4669706	0.86[AMR][1000 genomes]
rs4669709	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4669711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4669712	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4669713	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4669715	0.93[CEU][hapmap]
rs62118012	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6432183	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs6432184	0.94[CEU][hapmap]
rs6432185	0.89[AMR][1000 genomes]
rs6432186	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6706126	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6710031	0.94[CEU][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6713273	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6713382	0.82[AMR][1000 genomes]
rs6721445	1.00[CEU][hapmap];0.97[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6730673	0.90[YRI][hapmap]
rs6733312	1.00[CEU][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6735090	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6736240	0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs6749456	1.00[CEU][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6753875	0.81[AMR][1000 genomes]
rs6755196	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6755337	0.90[YRI][hapmap];0.87[AMR][1000 genomes]
rs6760802	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs7355446	1.00[CEU][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7355489	0.90[YRI][hapmap];0.87[AMR][1000 genomes]
rs753770	1.00[CEU][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7558664	0.90[YRI][hapmap]
rs7563468	0.93[YRI][hapmap];0.81[AMR][1000 genomes]
rs7563928	1.00[CEU][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7568064	0.85[YRI][hapmap]
rs7573458	0.92[EUR][1000 genomes]
rs7575837	0.85[YRI][hapmap];0.89[AMR][1000 genomes]
rs7593091	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9287728	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs965665	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs9712182	0.89[AMR][1000 genomes]
rs9808228	0.84[EUR][1000 genomes]
rs9967898	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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
rs4669710	PQLC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11450600-11466600	Weak transcription	NHLF	lung
2	chr2:11451600-11467000	Weak transcription	Primary B cells from cord blood	blood
3	chr2:11454400-11469800	Weak transcription	Fetal Brain Male	brain
4	chr2:11455000-11469200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:11455200-11466600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:11456000-11469400	Weak transcription	HSMM	muscle
7	chr2:11457200-11476400	Weak transcription	Fetal Intestine Small	intestine
8	chr2:11457400-11469800	Weak transcription	Hela-S3	cervix
9	chr2:11459800-11469400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:11460600-11469400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:11460800-11469800	Weak transcription	Fetal Lung	lung
12	chr2:11461000-11467200	Weak transcription	Right Ventricle	heart
13	chr2:11461000-11476400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:11461200-11469400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:11462400-11467600	Weak transcription	Left Ventricle	heart
16	chr2:11463000-11466600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:11464000-11466800	Weak transcription	A549	lung
18	chr2:11464200-11467200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:11464400-11466600	Weak transcription	Psoas Muscle	Psoas
20	chr2:11464400-11467200	Weak transcription	Ovary	ovary
21	chr2:11464400-11475200	Weak transcription	Aorta	Aorta
22	chr2:11464800-11466800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:11465200-11466800	Genic enhancers	HepG2	liver
24	chr2:11465200-11467800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:11465400-11466800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:11465400-11467200	Enhancers	Right Atrium	heart
27	chr2:11465400-11467800	Enhancers	Brain Anterior Caudate	brain
28	chr2:11465600-11467600	Enhancers	Brain Substantia Nigra	brain
29	chr2:11465800-11467400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:11466000-11466600	Enhancers	Brain Cingulate Gyrus	brain
31	chr2:11466000-11466600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:11466000-11466600	Enhancers	GM12878-XiMat	blood
33	chr2:11466000-11466600	Enhancers	HUVEC	blood vessel
34	chr2:11466000-11466800	Enhancers	Liver	Liver
35	chr2:11466000-11467200	Enhancers	Small Intestine	intestine
36	chr2:11466000-11467400	Enhancers	K562	blood
37	chr2:11466000-11467800	Enhancers	Adipose Nuclei	Adipose
38	chr2:11466000-11467800	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr2:11466000-11468600	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr2:11466200-11466600	Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr2:11466200-11466600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:11466200-11466600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr2:11466200-11466600	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr2:11466200-11467000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr2:11466200-11467000	Flanking Active TSS	NHDF-Ad	bronchial
46	chr2:11466200-11467200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:11466200-11469400	Weak transcription	Colon Smooth Muscle	Colon
48	chr2:11466400-11466600	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr2:11466400-11466600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:11466400-11466600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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