Variant report

Variant	rs3820082
Chromosome Location	chr1:46645524-46645525
allele	A/C
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	chr1:46645115-46645528	K562	blood:	n/a	n/a
2	CTCF	chr1:46645222-46645575	SK-N-SH_RA	brain:	n/a	chr1:46645387-46645403 chr1:46645388-46645401 chr1:46645386-46645404 chr1:46645381-46645402
3	SMC3	chr1:46644921-46645631	GM12878	blood:	n/a	chr1:46645388-46645402
4	HCFC1	chr1:46645209-46645547	K562	blood:	n/a	n/a
5	RAD21	chr1:46645068-46645609	H1-hESC	embryonic stem cell:	n/a	chr1:46645384-46645403 chr1:46645388-46645402
6	CTCF	chr1:46645257-46645537	Medullo	brain:	n/a	chr1:46645387-46645403 chr1:46645388-46645401 chr1:46645386-46645404 chr1:46645381-46645402
7	MAFK	chr1:46645153-46645588	K562	blood:	n/a	n/a
8	CTCF	chr1:46645144-46645668	K562	blood:	n/a	chr1:46645387-46645403 chr1:46645388-46645401 chr1:46645386-46645404 chr1:46645381-46645402
9	CTCF	chr1:46645168-46645615	GM12878	blood:	n/a	chr1:46645387-46645403 chr1:46645388-46645401 chr1:46645386-46645404 chr1:46645381-46645402
10	FOXA1	chr1:46645211-46645627	HepG2	liver:	n/a	n/a
11	CTCF	chr1:46645179-46645566	K562	blood:	n/a	chr1:46645387-46645403 chr1:46645388-46645401 chr1:46645386-46645404 chr1:46645381-46645402
12	MAZ	chr1:46645024-46645590	IMR90	lung:	n/a	n/a
13	EBF1	chr1:46645221-46645534	GM12878	blood:	n/a	n/a
14	RAD21	chr1:46644999-46646485	ECC-1	luminal epithelium:	n/a	chr1:46646103-46646115 chr1:46645384-46645403 chr1:46646103-46646113 chr1:46645996-46646009 chr1:46646101-46646114 chr1:46645388-46645402 chr1:46646098-46646117
15	MYC	chr1:46645175-46646283	MCF10A-Er-Src	breast:	n/a	n/a
16	RCOR1	chr1:46645213-46645634	K562	blood:	n/a	n/a
17	RAD21	chr1:46645065-46645651	SK-N-SH_RA	brain:	n/a	chr1:46645384-46645403 chr1:46645388-46645402
18	RCOR1	chr1:46645208-46645570	K562	blood:	n/a	n/a
19	SMC3	chr1:46644994-46646341	Hela-S3	cervix:	n/a	chr1:46646103-46646113 chr1:46646099-46646113 chr1:46645388-46645402 chr1:46646150-46646160
20	RUNX3	chr1:46645094-46645599	GM12878	blood:	n/a	n/a
21	FOXA2	chr1:46645223-46645536	A549	lung:	n/a	n/a
22	MYC	chr1:46645252-46646282	MCF10A-Er-Src	breast:	n/a	n/a
23	CUX1	chr1:46645147-46645570	GM12878	blood:	n/a	n/a
24	CTCF	chr1:46644664-46646368	SK-N-SH	brain:	n/a	chr1:46645387-46645403 chr1:46645388-46645401 chr1:46646100-46646113 chr1:46645386-46645404 chr1:46645381-46645402 chr1:46646097-46646115
25	CTCF	chr1:46645248-46645533	Pancreas_OC	pancreas:	n/a	chr1:46645387-46645403 chr1:46645388-46645401 chr1:46645386-46645404 chr1:46645381-46645402
26	STAT3	chr1:46645494-46646161	MCF10A-Er-Src	breast:	n/a	chr1:46645974-46645985 chr1:46645976-46645984
27	RAD21	chr1:46644954-46646547	HCT-116	colon:	n/a	chr1:46646103-46646115 chr1:46645384-46645403 chr1:46646103-46646113 chr1:46645996-46646009 chr1:46646101-46646114 chr1:46645388-46645402 chr1:46646098-46646117
28	ELK1	chr1:46645319-46646150	Hela-S3	cervix:	n/a	n/a
29	ZKSCAN1	chr1:46645156-46645541	Hela-S3	cervix:	n/a	n/a
30	CTCF	chr1:46645131-46645586	H1-hESC	embryonic stem cell:	n/a	chr1:46645387-46645403 chr1:46645388-46645401 chr1:46645386-46645404 chr1:46645381-46645402
31	CTCF	chr1:46645274-46645539	LNCaP	prostate:	n/a	chr1:46645387-46645403 chr1:46645388-46645401 chr1:46645386-46645404 chr1:46645381-46645402
32	RAD21	chr1:46644945-46646339	SK-N-SH	brain:	n/a	chr1:46646103-46646115 chr1:46645384-46645403 chr1:46646103-46646113 chr1:46645996-46646009 chr1:46646101-46646114 chr1:46645388-46645402 chr1:46646098-46646117
33	TEAD4	chr1:46644984-46645583	K562	blood:	n/a	n/a
34	CTCF	chr1:46645250-46645551	GM10266	blood:	n/a	chr1:46645387-46645403 chr1:46645388-46645401 chr1:46645386-46645404 chr1:46645381-46645402
35	RAD21	chr1:46645002-46645756	IMR90	lung:	n/a	chr1:46645384-46645403 chr1:46645388-46645402
36	SMC3	chr1:46645121-46645604	K562	blood:	n/a	chr1:46645388-46645402
37	RAD21	chr1:46645065-46645628	A549	lung:	n/a	chr1:46645384-46645403 chr1:46645388-46645402
38	CTCF	chr1:46645216-46645565	ECC-1	luminal epithelium:	n/a	chr1:46645387-46645403 chr1:46645388-46645401 chr1:46645386-46645404 chr1:46645381-46645402
39	CTCF	chr1:46645243-46645551	K562	blood:	n/a	chr1:46645387-46645403 chr1:46645388-46645401 chr1:46645386-46645404 chr1:46645381-46645402
40	RAD21	chr1:46645145-46645611	K562	blood:	n/a	chr1:46645384-46645403 chr1:46645388-46645402
41	NFIC	chr1:46645127-46645555	GM12878	blood:	n/a	n/a
42	RAD21	chr1:46645060-46645651	H1-hESC	embryonic stem cell:	n/a	chr1:46645384-46645403 chr1:46645388-46645402
43	MAZ	chr1:46645223-46646274	Hela-S3	cervix:	n/a	n/a
44	ZNF143	chr1:46645182-46645561	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr1:46645106-46645605	H1-hESC	embryonic stem cell:	n/a	chr1:46645387-46645403 chr1:46645388-46645401 chr1:46645386-46645404 chr1:46645381-46645402
46	MXI1	chr1:46645032-46645576	GM12878	blood:	n/a	n/a
47	RAD21	chr1:46645082-46646330	Hela-S3	cervix:	n/a	chr1:46646103-46646115 chr1:46645384-46645403 chr1:46646103-46646113 chr1:46645996-46646009 chr1:46646101-46646114 chr1:46645388-46645402 chr1:46646098-46646117
48	ZC3H11A	chr1:46645269-46645550	K562	blood:	n/a	n/a
49	RAD21	chr1:46645059-46645649	HepG2	liver:	n/a	chr1:46645384-46645403 chr1:46645388-46645402
50	CTCF	chr1:46645191-46645558	ECC-1	luminal epithelium:	n/a	chr1:46645387-46645403 chr1:46645388-46645401 chr1:46645386-46645404 chr1:46645381-46645402

No.	Distal block	Cell Line	Cell type
1	chr1:46644247..46646808-chr1:46647316..46649049,2	MCF-7	breast:
2	chr1:46596322..46599867-chr1:46644378..46648277,6	K562	blood:
3	chr1:46644984..46646152-chr1:46663414..46664416,4	MCF-7	breast:
4	chr1:46502754..46504889-chr1:46644727..46646775,2	MCF-7	breast:
5	chr1:46645330..46646916-chr1:46688561..46690011,13	MCF-7	breast:
6	chr1:46640707..46642746-chr1:46643622..46645846,4	K562	blood:
7	chr1:46358179..46359900-chr1:46645424..46647208,2	MCF-7	breast:
8	chr1:46592691..46601867-chr1:46642778..46650670,25	MCF-7	breast:
9	chr1:46502426..46503494-chr1:46644975..46645543,3	MCF-7	breast:
10	chr1:46645378..46646366-chr1:46664542..46665185,2	MCF-7	breast:
11	chr1:46639014..46642746-chr1:46643175..46646686,4	K562	blood:
12	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
13	chr1:46645047..46645865-chr1:46688938..46689650,2	MCF-7	breast:
14	chr1:46636993..46639249-chr1:46644481..46646542,2	MCF-7	breast:
15	chr1:46502434..46503605-chr1:46644931..46645927,6	MCF-7	breast:
16	chr1:46643862..46647366-chr1:46664036..46667027,3	K562	blood:
17	chr1:46587981..46590645-chr1:46643628..46646166,3	MCF-7	breast:
18	chr1:46500117..46505906-chr1:46642218..46647717,9	K562	blood:
19	chr1:46506118..46508735-chr1:46643577..46646194,3	K562	blood:
20	chr1:46645259..46646856-chr1:46688566..46690033,15	K562	blood:
21	chr1:46505537..46508242-chr1:46645160..46646732,2	MCF-7	breast:
22	chr1:46501987..46504531-chr1:46644237..46646306,43	K562	blood:
23	chr1:46645371..46647493-chr1:46686885..46689393,2	MCF-7	breast:

Variant related genes	Relation type
TSPAN1	TF binding region
ENSG00000250719	TF binding region
PIK3R3	TF binding region
ENSG00000250719	Chromatin interaction
ENSG00000085998	Chromatin interaction
ENSG00000117461	Chromatin interaction
ENSG00000227857	Chromatin interaction
ENSG00000117472	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10493121	0.84[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11211258	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11211259	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12029134	0.81[EUR][1000 genomes]
rs12029936	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12064594	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12134419	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1618281	0.84[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes]
rs3753363	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3845300	0.82[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3845301	0.91[JPT][hapmap]
rs3855959	0.86[JPT][hapmap]
rs6661071	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6671303	0.86[JPT][hapmap]
rs7512966	0.89[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs7536272	0.95[CEU][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1006530	chr1:46544842-46655484	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv534949	chr1:46544842-46655484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3820082	CYP4X1	cis	cerebellum	SCAN
rs3820082	IPP	cis	lymphoblastoid	seeQTL
rs3820082	CMPK1	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46637800-46649600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:46639400-46645600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:46639400-46653800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:46639600-46652800	Weak transcription	Brain Germinal Matrix	brain
5	chr1:46639800-46645800	Weak transcription	Colonic Mucosa	Colon
6	chr1:46640600-46648800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:46640800-46645600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr1:46640800-46656400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:46641000-46645600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:46641000-46645800	Weak transcription	Gastric	stomach
11	chr1:46641000-46648600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:46641200-46645800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:46641200-46645800	Weak transcription	Esophagus	oesophagus
14	chr1:46641200-46645800	Weak transcription	NHDF-Ad	bronchial
15	chr1:46641200-46646600	Weak transcription	Fetal Kidney	kidney
16	chr1:46641200-46647200	Weak transcription	HSMM	muscle
17	chr1:46641200-46647400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:46641200-46647600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:46641200-46648800	Weak transcription	HSMMtube	muscle
20	chr1:46641200-46649000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:46641400-46648600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:46642200-46645800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:46642200-46646200	Weak transcription	Lung	lung
24	chr1:46642200-46646800	Weak transcription	Spleen	Spleen
25	chr1:46642200-46648400	Weak transcription	Left Ventricle	heart
26	chr1:46642400-46648800	Weak transcription	Right Atrium	heart
27	chr1:46642400-46648800	Weak transcription	Right Ventricle	heart
28	chr1:46643800-46645600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:46644400-46648400	Weak transcription	Psoas Muscle	Psoas
30	chr1:46644600-46646200	Enhancers	Fetal Intestine Small	intestine
31	chr1:46644800-46645600	Enhancers	Primary B cells from peripheral blood	blood
32	chr1:46644800-46645600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr1:46644800-46646000	Enhancers	Fetal Intestine Large	intestine
34	chr1:46644800-46646400	Enhancers	Fetal Muscle Leg	muscle
35	chr1:46644800-46651400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr1:46645000-46645600	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr1:46645000-46645600	Enhancers	Colon Smooth Muscle	Colon
38	chr1:46645000-46645600	Enhancers	Fetal Lung	lung
39	chr1:46645000-46645600	Enhancers	HMEC	breast
40	chr1:46645000-46645800	Enhancers	Muscle Satellite Cultured Cells	--
41	chr1:46645000-46645800	Enhancers	Adipose Nuclei	Adipose
42	chr1:46645000-46646000	Enhancers	Fetal Heart	heart
43	chr1:46645000-46646000	Enhancers	GM12878-XiMat	blood
44	chr1:46645000-46646200	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr1:46645000-46646200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:46645000-46646200	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr1:46645000-46646200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr1:46645000-46646200	Enhancers	HepG2	liver
49	chr1:46645000-46646400	Enhancers	Brain Angular Gyrus	brain
50	chr1:46645000-46646400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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