Variant report

Variant	rs6733312
Chromosome Location	chr2:11446507-11446508
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr2:11446024-11446635	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr2:11445807-11446698	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr2:11445765-11446632	SK-N-SH	brain:	n/a	n/a
4	HNF4A	chr2:11446189-11446525	HepG2	liver:	n/a	chr2:11446364-11446379
5	PBX3	chr2:11445867-11446569	SK-N-SH	brain:	n/a	n/a
6	MEF2A	chr2:11446004-11446569	SK-N-SH	brain:	n/a	n/a
7	EP300	chr2:11445968-11446669	SK-N-SH	brain:	n/a	n/a
8	MAFK	chr2:11446098-11446528	IMR90	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:11443856..11445730-chr2:11445772..11448144,2	K562	blood:
2	chr2:11437773..11439523-chr2:11445218..11447388,2	K562	blood:
3	chr2:11444512..11447438-chr2:11450182..11452688,2	K562	blood:
4	chr2:11444757..11447160-chr2:11453898..11455416,2	MCF-7	breast:
5	chr2:11435287..11437143-chr2:11445238..11447670,2	K562	blood:
6	chr2:11446328..11449302-chr2:11482839..11485533,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-E2F6-1	chr2:11446486-11446891	NONHSAT069155

No data

Variant related genes	Relation type
ENSG00000230154	TF binding region
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10178332	0.94[CEU][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[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];0.82[YRI][hapmap];0.82[AMR][1000 genomes]
rs10203916	1.00[CEU][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes]
rs10205944	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs10206334	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10210600	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10454126	1.00[CEU][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10754957	0.81[EUR][1000 genomes]
rs10929730	0.89[EUR][1000 genomes]
rs10929732	0.87[YRI][hapmap]
rs11681822	0.94[AMR][1000 genomes]
rs11694729	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[EUR][1000 genomes]
rs11695377	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs12692434	1.00[CEU][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12692435	0.90[YRI][hapmap];0.81[AFR][1000 genomes];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	0.87[YRI][hapmap];0.87[AMR][1000 genomes]
rs12994807	0.81[YRI][hapmap];0.89[AMR][1000 genomes]
rs13014721	0.90[AMR][1000 genomes]
rs13015560	0.82[CEU][hapmap]
rs13017021	0.86[CEU][hapmap]
rs1515224	0.85[EUR][1000 genomes]
rs1562748	1.00[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[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	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2084577	1.00[CEU][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2100228	0.86[EUR][1000 genomes]
rs2122384	0.86[YRI][hapmap];0.89[AMR][1000 genomes]
rs2167126	0.83[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];0.90[YRI][hapmap];0.84[EUR][1000 genomes]
rs4303693	0.94[CEU][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4668720	0.84[YRI][hapmap]
rs4669699	0.81[EUR][1000 genomes]
rs4669706	0.86[AMR][1000 genomes]
rs4669709	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4669710	1.00[CEU][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4669711	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4669712	0.84[AMR][1000 genomes]
rs4669713	1.00[CEU][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes]
rs4669715	0.93[CEU][hapmap]
rs62118012	0.90[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];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6706126	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6710031	0.94[CEU][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6713273	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6713382	0.82[AMR][1000 genomes]
rs6721445	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6730673	0.86[YRI][hapmap]
rs6735090	0.86[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];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6753875	0.81[AMR][1000 genomes]
rs6755196	1.00[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6755337	0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs6760802	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs7355446	1.00[CEU][hapmap];0.86[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];0.87[YRI][hapmap];0.94[AMR][1000 genomes]
rs7568064	0.84[YRI][hapmap]
rs7573458	0.92[EUR][1000 genomes]
rs7575837	0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7593091	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[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
rs6733312	PQLC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11424800-11455200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:11433600-11446800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:11433600-11448000	Weak transcription	Right Ventricle	heart
4	chr2:11439200-11453000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:11442800-11447800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:11443400-11447200	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr2:11443400-11447200	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr2:11443600-11446600	Weak transcription	Fetal Intestine Large	intestine
9	chr2:11443600-11446800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:11443600-11447000	Enhancers	Adipose Nuclei	Adipose
11	chr2:11443800-11449400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:11444000-11447400	Enhancers	Colon Smooth Muscle	Colon
13	chr2:11444000-11449800	Weak transcription	Aorta	Aorta
14	chr2:11444000-11458600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:11444200-11447400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:11444600-11446800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:11444600-11447000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr2:11444600-11447800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr2:11444800-11447600	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr2:11444800-11448000	Enhancers	NHDF-Ad	bronchial
21	chr2:11444800-11454600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:11445000-11465200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:11445200-11450200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr2:11445400-11447200	Enhancers	Muscle Satellite Cultured Cells	--
25	chr2:11445400-11447200	Enhancers	HSMM	muscle
26	chr2:11445400-11460200	Weak transcription	Left Ventricle	heart
27	chr2:11445600-11447000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:11445600-11447000	Enhancers	Fetal Intestine Small	intestine
29	chr2:11445600-11447000	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr2:11445600-11447200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:11445600-11447200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:11445600-11447200	Enhancers	Osteobl	bone
33	chr2:11445600-11447400	Enhancers	NHLF	lung
34	chr2:11445600-11447600	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr2:11445800-11446800	Weak transcription	Psoas Muscle	Psoas
36	chr2:11445800-11447000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:11445800-11447000	Enhancers	Duodenum Mucosa	Duodenum
38	chr2:11445800-11447200	Enhancers	Fetal Stomach	stomach
39	chr2:11445800-11448800	Weak transcription	NHEK	skin
40	chr2:11445800-11449800	Weak transcription	Lung	lung
41	chr2:11446000-11446800	Weak transcription	Fetal Heart	heart
42	chr2:11446000-11446800	Enhancers	HMEC	breast
43	chr2:11446000-11446800	Weak transcription	HSMMtube	muscle
44	chr2:11446000-11447000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:11446000-11447000	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr2:11446000-11447000	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr2:11446000-11447000	Enhancers	Fetal Lung	lung
48	chr2:11446000-11447200	Enhancers	Stomach Smooth Muscle	stomach
49	chr2:11446000-11447200	Enhancers	A549	lung
50	chr2:11446000-11448400	Enhancers	HepG2	liver

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