Variant report

Variant	rs9961065
Chromosome Location	chr18:43653327-43653328
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr18:43653028-43654282	SK-N-SH	brain:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
2	CTCF	chr18:43653200-43653350	GM12868	blood:	n/a	n/a
3	CTCF	chr18:43653311-43654265	A549	lung:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
4	SMC3	chr18:43653141-43654309	SK-N-SH	brain:	n/a	chr18:43653893-43653907
5	RAD21	chr18:43653162-43654276	SK-N-SH	brain:	n/a	chr18:43653889-43653908

Variant related genes	Relation type
PSTPIP2	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11082509	0.82[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11082510	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11659357	0.89[EUR][1000 genomes]
rs11659478	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11659795	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11661945	0.83[EUR][1000 genomes]
rs11664764	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11872954	0.85[EUR][1000 genomes]
rs11872985	0.85[EUR][1000 genomes]
rs11874712	0.87[EUR][1000 genomes]
rs12954944	1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13381709	1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1800636	1.00[JPT][hapmap];0.95[YRI][hapmap]
rs1800637	1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1800639	1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1800640	1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2298787	1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28457840	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504655	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28699609	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34907121	0.90[EUR][1000 genomes]
rs35507656	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765636	1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075249	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56181324	0.91[EUR][1000 genomes]
rs62096500	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7230064	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7235373	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244921	1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7244950	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8083998	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8085444	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8085743	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8088881	1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8089150	1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8091452	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8092674	1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8093880	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8094902	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8095031	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8095608	1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8097521	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9304326	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304327	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304328	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9783884	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9783886	1.00[JPT][hapmap];0.96[YRI][hapmap]
rs9783887	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9783888	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9944637	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9944659	0.86[ASN][1000 genomes]
rs9945606	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9945751	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9947908	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9954278	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9962380	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9962458	0.91[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	nsv1064882	chr18:43558343-43687674	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543693	chr18:43558343-43687674	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1062024	chr18:43589516-43749410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv543694	chr18:43589516-43749410	Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43651400-43657400	Weak transcription	A549	lung
2	chr18:43651600-43657600	Weak transcription	Dnd41	blood
3	chr18:43652200-43653400	Flanking Active TSS	Duodenum Mucosa	Duodenum
4	chr18:43652200-43653600	Enhancers	Fetal Heart	heart
5	chr18:43652200-43659600	Weak transcription	Small Intestine	intestine
6	chr18:43652400-43653400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr18:43652600-43653400	Enhancers	Primary hematopoietic stem cells	blood
8	chr18:43652600-43653400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr18:43652600-43653400	Weak transcription	Fetal Kidney	kidney
10	chr18:43652600-43653600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr18:43652600-43653600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr18:43652600-43653600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr18:43652600-43653600	Enhancers	Fetal Brain Female	brain
14	chr18:43652600-43653600	Weak transcription	Fetal Lung	lung
15	chr18:43652600-43653600	Enhancers	Left Ventricle	heart
16	chr18:43652600-43653600	Enhancers	Pancreas	Pancrea
17	chr18:43652600-43653600	Enhancers	Right Ventricle	heart
18	chr18:43652600-43653600	Enhancers	Stomach Mucosa	stomach
19	chr18:43652600-43653600	Enhancers	Spleen	Spleen
20	chr18:43652600-43653800	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr18:43652600-43653800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr18:43652600-43653800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr18:43652600-43653800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr18:43652600-43653800	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr18:43652600-43653800	Enhancers	Fetal Thymus	thymus
26	chr18:43652600-43654200	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr18:43652600-43654200	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr18:43652600-43654200	Enhancers	HMEC	breast
29	chr18:43652600-43656800	Weak transcription	NHEK	skin
30	chr18:43652600-43657000	Weak transcription	GM12878-XiMat	blood
31	chr18:43652600-43657400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr18:43652600-43657400	Weak transcription	Brain Anterior Caudate	brain
33	chr18:43652600-43657400	Weak transcription	Thymus	Thymus
34	chr18:43652600-43657400	Weak transcription	HSMMtube	muscle
35	chr18:43652600-43657600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr18:43652600-43657600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr18:43652600-43657600	Weak transcription	Brain Substantia Nigra	brain
38	chr18:43652600-43657600	Weak transcription	Right Atrium	heart
39	chr18:43652600-43657600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr18:43652600-43657800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr18:43652600-43660000	Weak transcription	Brain Angular Gyrus	brain
42	chr18:43652600-43662200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr18:43652600-43662600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr18:43652600-43663000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr18:43652600-43663200	Weak transcription	Esophagus	oesophagus
46	chr18:43652600-43665000	Weak transcription	Aorta	Aorta
47	chr18:43652800-43653400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr18:43652800-43653400	Active TSS	Colonic Mucosa	Colon
49	chr18:43652800-43653400	Bivalent Enhancer	Fetal Muscle Leg	muscle
50	chr18:43652800-43653400	Weak transcription	Lung	lung

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