Variant report

Variant	rs12533694
Chromosome Location	chr7:107102817-107102818
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107102189..107104759-chr7:107219342..107222383,3	MCF-7	breast:
2	chr7:107101908..107103603-chr7:107121771..107123430,2	K562	blood:
3	chr7:107094353..107098308-chr7:107101232..107104487,5	K562	blood:
4	chr7:107101147..107103872-chr7:107140703..107142303,2	K562	blood:
5	chr7:107101145..107103581-chr7:107110097..107112190,2	K562	blood:

Variant related genes	Relation type
ENSG00000075790	Chromatin interaction
ENSG00000172209	Chromatin interaction
ENSG00000272854	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10464499	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10464620	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10953541	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes]
rs11532774	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11766060	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs11766131	0.89[ASN][1000 genomes]
rs11770061	0.89[ASN][1000 genomes]
rs12056231	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12532447	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12532849	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12534124	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12535038	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12535761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12539895	0.93[ASN][1000 genomes]
rs13234124	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17403088	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17404067	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17481621	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17481842	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17482494	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17482543	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17486	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1978085	0.97[ASN][1000 genomes]
rs2249043	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2283041	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299428	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2395880	0.89[ASN][1000 genomes]
rs2395881	0.89[ASN][1000 genomes]
rs2894459	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs34084719	0.97[ASN][1000 genomes]
rs34523267	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3779497	0.90[ASN][1000 genomes]
rs4515482	0.89[ASN][1000 genomes]
rs4727683	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4730248	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4730250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56949084	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6945784	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6947674	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6955488	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6957186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6958969	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6964395	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6964966	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6976759	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6979198	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6979368	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs763386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7784906	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7785085	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7785962	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes]
rs7797791	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7801317	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7807154	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8180747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825788	chr7:106897237-107136320	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1024793	chr7:106900877-107170312	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv1832266	chr7:106961882-107136320	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv1019963	chr7:107033342-107188641	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv539052	chr7:107033342-107188641	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12533694	GPR22	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107028200-107103800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr7:107035800-107133000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr7:107052600-107126400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr7:107067600-107119800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:107068400-107104000	Weak transcription	Pancreas	Pancrea
6	chr7:107073000-107103600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr7:107079600-107108600	Weak transcription	Right Ventricle	heart
8	chr7:107081200-107103600	Weak transcription	Adipose Nuclei	Adipose
9	chr7:107082800-107104200	Weak transcription	Left Ventricle	heart
10	chr7:107082800-107109000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr7:107083400-107104200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr7:107083400-107104600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr7:107083400-107115400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:107084400-107109200	Weak transcription	Fetal Intestine Large	intestine
15	chr7:107087600-107103600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr7:107087600-107104000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr7:107087800-107103400	Weak transcription	Aorta	Aorta
18	chr7:107087800-107103600	Weak transcription	K562	blood
19	chr7:107087800-107112000	Weak transcription	NHDF-Ad	bronchial
20	chr7:107088000-107103600	Weak transcription	HSMMtube	muscle
21	chr7:107088000-107103800	Weak transcription	HMEC	breast
22	chr7:107088000-107103800	Weak transcription	NHEK	skin
23	chr7:107088600-107126000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr7:107090000-107114600	Weak transcription	Primary T cells from cord blood	blood
25	chr7:107090800-107104800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:107090800-107146000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr7:107091000-107145800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr7:107091600-107104000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr7:107091800-107103400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr7:107094400-107103600	Weak transcription	HUVEC	blood vessel
31	chr7:107094400-107103800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr7:107097000-107112200	Weak transcription	Fetal Lung	lung
33	chr7:107097400-107103400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr7:107097400-107104400	Weak transcription	Fetal Stomach	stomach
35	chr7:107098000-107108000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr7:107098200-107103000	Weak transcription	Fetal Intestine Small	intestine
37	chr7:107098800-107103600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:107098800-107132600	Weak transcription	Primary B cells from cord blood	blood
39	chr7:107099200-107104000	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr7:107099200-107104200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr7:107099600-107110400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr7:107100000-107104400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr7:107100200-107103800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr7:107101800-107105600	Enhancers	Fetal Heart	heart
45	chr7:107102200-107105600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr7:107102400-107103000	Enhancers	Brain Hippocampus Middle	brain
47	chr7:107102400-107103000	Enhancers	Brain Substantia Nigra	brain
48	chr7:107102400-107103600	Enhancers	Brain Cingulate Gyrus	brain
49	chr7:107102600-107103200	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr7:107102600-107103200	Weak transcription	Brain Anterior Caudate	brain

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