Variant report

Variant	rs3765636
Chromosome Location	chr18:43653660-43653661
allele	G/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	MYC	chr18:43653578-43654015	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr18:43653585-43654152	ECC-1	luminal epithelium:	n/a	chr18:43653889-43653908
3	ZNF384	chr18:43653553-43654003	K562	blood:	n/a	n/a
4	CTCF	chr18:43653566-43653677	NHEK	skin:	n/a	n/a
5	CTCF	chr18:43653592-43653670	Lung_OC	lung:	n/a	n/a
6	RAD21	chr18:43653505-43654171	HCT-116	colon:	n/a	chr18:43653889-43653908
7	CTCF	chr18:43653028-43654282	SK-N-SH	brain:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
8	POLR2A	chr18:43653627-43653670	Hela-S3	cervix:	n/a	n/a
9	RAD21	chr18:43653626-43654171	A549	lung:	n/a	chr18:43653889-43653908
10	CTCF	chr18:43653493-43654260	HCT-116	colon:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
11	CTCF	chr18:43653520-43653670	AoAF	blood vessel:	n/a	n/a
12	CTCF	chr18:43653520-43653670	HEK293	kidney:	n/a	n/a
13	CTCF	chr18:43653540-43653690	GM12875	blood:	n/a	n/a
14	CTCF	chr18:43653475-43653976	H1-hESC	embryonic stem cell:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
15	CTCF	chr18:43653660-43653810	WI-38	lung:	n/a	n/a
16	CTCF	chr18:43653559-43653684	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr18:43653540-43653670	H1-hESC	embryonic stem cell:	n/a	n/a
18	RAD21	chr18:43653596-43654074	GM12878	blood:	n/a	chr18:43653889-43653908
19	RAD21	chr18:43653350-43654199	ECC-1	luminal epithelium:	n/a	chr18:43653889-43653908
20	CTCF	chr18:43653311-43654265	A549	lung:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
21	POLR2A	chr18:43653639-43654126	HepG2	liver:	n/a	n/a
22	RAD21	chr18:43653519-43654088	Hela-S3	cervix:	n/a	chr18:43653889-43653908
23	CTCF	chr18:43653520-43653670	HPF	lung:	n/a	n/a
24	RAD21	chr18:43653495-43654119	SK-N-SH_RA	brain:	n/a	chr18:43653889-43653908
25	RAD21	chr18:43653480-43654108	H1-hESC	embryonic stem cell:	n/a	chr18:43653889-43653908
26	RAD21	chr18:43653640-43654076	K562	blood:	n/a	chr18:43653889-43653908
27	SMC3	chr18:43653141-43654309	SK-N-SH	brain:	n/a	chr18:43653893-43653907
28	CTCF	chr18:43653520-43653670	Hela-S3	cervix:	n/a	n/a
29	RAD21	chr18:43653617-43654167	HepG2	liver:	n/a	chr18:43653889-43653908
30	RAD21	chr18:43653613-43654150	MCF-7	breast:	n/a	chr18:43653889-43653908
31	CTCF	chr18:43653599-43654115	K562	blood:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
32	RAD21	chr18:43653162-43654276	SK-N-SH	brain:	n/a	chr18:43653889-43653908
33	CTCF	chr18:43653560-43653710	GM12872	blood:	n/a	n/a
34	CTCF	chr18:43653539-43654120	GM12878	blood:	n/a	chr18:43653886-43653907 chr18:43653891-43653909 chr18:43653894-43653904 chr18:43653892-43653908
35	CTCF	chr18:43653540-43653690	GM12873	blood:	n/a	n/a
36	RAD21	chr18:43653367-43654180	HCT-116	colon:	n/a	chr18:43653889-43653908
37	CTCF	chr18:43653581-43653666	GM12892	blood:	n/a	n/a
38	CTCF	chr18:43653540-43653690	WERI-Rb-1	eye:	n/a	n/a
39	POLR2A	chr18:43653516-43653675	MCF-7	breast:	n/a	n/a
40	RAD21	chr18:43653417-43654034	H1-hESC	embryonic stem cell:	n/a	chr18:43653889-43653908
41	RAD21	chr18:43653607-43654155	A549	lung:	n/a	chr18:43653889-43653908
42	RAD21	chr18:43653360-43654131	H1-hESC	embryonic stem cell:	n/a	chr18:43653889-43653908
43	POLR2A	chr18:43653636-43654118	MCF10A-Er-Src	breast:	n/a	n/a
44	CTCF	chr18:43653560-43653710	GM12871	blood:	n/a	n/a
45	SMC3	chr18:43653526-43654133	Hela-S3	cervix:	n/a	chr18:43653893-43653907
46	RAD21	chr18:43653616-43654093	IMR90	lung:	n/a	chr18:43653889-43653908

No.	Distal block	Cell Line	Cell type
1	chr18:43553826..43554616-chr18:43653485..43654035,3	MCF-7	breast:
2	chr18:43553938..43554665-chr18:43653434..43654381,2	MCF-7	breast:
3	chr18:43244763..43245742-chr18:43653653..43654356,2	MCF-7	breast:
4	chr18:43244798..43245740-chr18:43653443..43653974,2	K562	blood:

Variant related genes	Relation type
PSTPIP2	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11082509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.98[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	0.90[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	0.86[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	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12954944	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13381709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1800636	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs1800637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1800639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1800640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2298787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28457840	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504655	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28699609	0.86[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	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[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	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7227508	1.00[CHB][hapmap]
rs7230064	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7231846	1.00[CHB][hapmap]
rs7235373	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7244950	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8083998	0.86[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	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8088881	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8089150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8091452	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8092674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8093880	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8094902	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8095031	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8095608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[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	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304327	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304328	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9783884	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9783886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[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	0.86[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	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9961065	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]
rs9962380	0.84[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:120 , 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	chr18:43652200-43659600	Weak transcription	Small Intestine	intestine
4	chr18:43652600-43653800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr18:43652600-43653800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr18:43652600-43653800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr18:43652600-43653800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr18:43652600-43653800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr18:43652600-43653800	Enhancers	Fetal Thymus	thymus
10	chr18:43652600-43654200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr18:43652600-43654200	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr18:43652600-43654200	Enhancers	HMEC	breast
13	chr18:43652600-43656800	Weak transcription	NHEK	skin
14	chr18:43652600-43657000	Weak transcription	GM12878-XiMat	blood
15	chr18:43652600-43657400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr18:43652600-43657400	Weak transcription	Brain Anterior Caudate	brain
17	chr18:43652600-43657400	Weak transcription	Thymus	Thymus
18	chr18:43652600-43657400	Weak transcription	HSMMtube	muscle
19	chr18:43652600-43657600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr18:43652600-43657600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr18:43652600-43657600	Weak transcription	Brain Substantia Nigra	brain
22	chr18:43652600-43657600	Weak transcription	Right Atrium	heart
23	chr18:43652600-43657600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr18:43652600-43657800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr18:43652600-43660000	Weak transcription	Brain Angular Gyrus	brain
26	chr18:43652600-43662200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr18:43652600-43662600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr18:43652600-43663000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr18:43652600-43663200	Weak transcription	Esophagus	oesophagus
30	chr18:43652600-43665000	Weak transcription	Aorta	Aorta
31	chr18:43652800-43653800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr18:43652800-43653800	Enhancers	Primary B cells from cord blood	blood
33	chr18:43652800-43653800	Enhancers	Primary T cells from cord blood	blood
34	chr18:43652800-43653800	Enhancers	Primary T cells fromperipheralblood	blood
35	chr18:43652800-43653800	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr18:43652800-43653800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr18:43652800-43653800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr18:43652800-43653800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr18:43652800-43653800	Enhancers	Adipose Nuclei	Adipose
40	chr18:43652800-43654200	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr18:43652800-43654200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr18:43652800-43654200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr18:43652800-43654200	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr18:43652800-43654200	Enhancers	NHLF	lung
45	chr18:43652800-43654200	Enhancers	Osteobl	bone
46	chr18:43652800-43654600	Enhancers	Liver	Liver
47	chr18:43652800-43656200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr18:43652800-43657200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr18:43652800-43657400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr18:43652800-43657400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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