Variant report

Variant	rs771572
Chromosome Location	chr3:101659656-101659657
allele	A/G
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	chr3:101659559-101659694	MCF10A-Er-Src	breast:	n/a	n/a
2	EP300	chr3:101659325-101659997	SK-N-SH_RA	brain:	n/a	chr3:101659577-101659591
3	SPI1	chr3:101659312-101659800	GM12891	blood:	n/a	n/a
4	EP300	chr3:101659419-101659902	K562	blood:	n/a	chr3:101659577-101659591
5	REST	chr3:101659486-101659816	SK-N-SH	brain:	n/a	n/a
6	ATF1	chr3:101659462-101659881	K562	blood:	n/a	n/a
7	FOS	chr3:101659414-101659741	MCF10A-Er-Src	breast:	n/a	n/a
8	GATA3	chr3:101659527-101659891	SH-SY5Y	brain:	n/a	chr3:101659579-101659589
9	FOXP2	chr3:101659494-101659793	SK-N-MC	brain:	n/a	n/a
10	STAT3	chr3:101659361-101659716	MCF10A-Er-Src	breast:	n/a	n/a
11	EP300	chr3:101658998-101660187	SK-N-SH	brain:	n/a	chr3:101659273-101659287 chr3:101659577-101659591
12	ZBTB33	chr3:101659223-101659980	SK-N-SH	brain:	n/a	n/a
13	NFIC	chr3:101659142-101660023	SK-N-SH	brain:	n/a	chr3:101659513-101659530
14	GTF2F1	chr3:101659462-101659828	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr3:101659415-101659716	HUVEC	blood vessel:	n/a	n/a
16	EP300	chr3:101659334-101659812	Hela-S3	cervix:	n/a	chr3:101659577-101659591
17	RAD21	chr3:101659379-101659891	SK-N-SH_RA	brain:	n/a	n/a
18	MXI1	chr3:101659209-101660074	IMR90	lung:	n/a	n/a
19	MYC	chr3:101659340-101659778	K562	blood:	n/a	n/a
20	YY1	chr3:101659242-101659931	SK-N-SH	brain:	n/a	n/a
21	E2F4	chr3:101659466-101659679	MCF10A-Er-Src	breast:	n/a	n/a
22	RXRA	chr3:101659081-101659981	SK-N-SH	brain:	n/a	chr3:101659278-101659287 chr3:101659272-101659281 chr3:101659232-101659241
23	TCF12	chr3:101658899-101660840	SK-N-SH	brain:	n/a	chr3:101660769-101660778
24	POLR2A	chr3:101659298-101659860	U87	brain:	n/a	n/a
25	SMC3	chr3:101659431-101659787	Hela-S3	cervix:	n/a	n/a
26	GATA3	chr3:101657942-101660957	SK-N-SH	brain:	n/a	chr3:101659283-101659299 chr3:101659288-101659299 chr3:101659281-101659302 chr3:101659579-101659589 chr3:101659930-101659938 chr3:101659288-101659295 chr3:101659288-101659295 chr3:101659288-101659295 chr3:101659286-101659295 chr3:101659286-101659296
27	RUNX3	chr3:101659351-101660854	GM12878	blood:	n/a	n/a
28	STAT3	chr3:101659291-101659819	MCF10A-Er-Src	breast:	n/a	n/a
29	EP300	chr3:101659160-101659972	SK-N-SH_RA	brain:	n/a	chr3:101659273-101659287 chr3:101659577-101659591
30	POLR2A	chr3:101659255-101659860	SK-N-MC	brain:	n/a	n/a
31	SPI1	chr3:101659343-101659759	HL-60	blood:	n/a	n/a
32	TEAD4	chr3:101659259-101659744	ECC-1	luminal epithelium:	n/a	n/a
33	PBX3	chr3:101659111-101660973	SK-N-SH	brain:	n/a	n/a
34	EP300	chr3:101658979-101660979	SK-N-SH	brain:	n/a	chr3:101659273-101659287 chr3:101659577-101659591 chr3:101660769-101660779
35	SPI1	chr3:101659372-101659733	GM12878	blood:	n/a	n/a
36	STAT3	chr3:101659305-101659786	MCF10A-Er-Src	breast:	n/a	n/a
37	JUND	chr3:101659001-101660087	SK-N-SH	brain:	n/a	n/a
38	FOS	chr3:101659342-101659811	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr3:101659503-101659703	MCF10A-Er-Src	breast:	n/a	n/a
40	FOSL2	chr3:101659260-101659916	SK-N-SH	brain:	n/a	n/a
41	FOS	chr3:101659311-101659799	MCF10A-Er-Src	breast:	n/a	n/a
42	KAP1	chr3:101659365-101659986	U2OS	brain:	n/a	n/a
43	CTCF	chr3:101659580-101659730	AG10803	skin:	n/a	n/a
44	TCF7L2	chr3:101659458-101659826	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr3:101659315-101659898	U87	brain:	n/a	n/a
46	FOS	chr3:101659291-101660546	MCF10A-Er-Src	breast:	n/a	n/a
47	EBF1	chr3:101659554-101659757	GM12878	blood:	n/a	n/a
48	TEAD4	chr3:101659024-101660188	SK-N-SH	brain:	n/a	n/a
49	NFIC	chr3:101659198-101659855	ECC-1	luminal epithelium:	n/a	chr3:101659513-101659530
50	MAZ	chr3:101659484-101659892	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:101659630-101659680	GM19239	blood:	n/a
2	chr3:101659630-101659680	HRPEpiC	eye:	n/a
3	chr3:101659630-101659680	AG04450	lung:	fetal
4	chr3:101659630-101659680	HEEpiC	esophagus:	n/a
5	chr3:101659630-101659680	AG09319	gingival:	n/a
6	chr3:101659630-101659680	HIPEpiC	eye:	n/a
7	chr3:101659630-101659680	AG09309	skin:	n/a
8	chr3:101659630-101659680	NT2-D1	testis:	n/a
9	chr3:101659630-101659680	SK-N-MC	brain:	n/a
10	chr3:101659630-101659680	GM12892	blood:	n/a
11	chr3:101659630-101659680	U87	brain:	n/a
12	chr3:101659630-101659680	HNPCEpiC	eye:	n/a
13	chr3:101659630-101659680	LNCaP	prostate:	n/a
14	chr3:101659630-101659680	MCF10A-Er-Src	breast:	n/a
15	chr3:101659630-101659680	HCM	heart:	n/a
16	chr3:101659630-101659680	NB4	blood:	n/a
17	chr3:101659630-101659680	ECC-1	luminal epithelium:	n/a
18	chr3:101659630-101659680	H1-hESC	embryonic stem cell:	embryo
19	chr3:101659630-101659680	Hepatocyte	liver:	n/a
20	chr3:101659630-101659680	SK-N-SH	brain:	n/a
21	chr3:101659630-101659680	HPAEpiC	pulmonary alveolar:	n/a
22	chr3:101659630-101659680	SAEC	small airway:	n/a
23	chr3:101659630-101659680	PFSK-1	brain:	n/a
24	chr3:101659630-101659680	HEK293	kidney:	embryo
25	chr3:101659630-101659680	Jurkat	blood:	n/a
26	chr3:101659630-101659680	HRCEpiC	kidney:	n/a
27	chr3:101659630-101659680	AG04449	skin:	fetal
28	chr3:101659630-101659680	K562	blood:	n/a
29	chr3:101659630-101659680	A549	lung:	n/a
30	chr3:101659630-101659680	ProgFib	skin:	n/a
31	chr3:101659630-101659680	HL-60	blood:	n/a
32	chr3:101659630-101659680	MCF-7	breast:	n/a
33	chr3:101659630-101659680	IMR90	lung:	fetal
34	chr3:101659630-101659680	HUVEC	blood vessel:	n/a
35	chr3:101659630-101659680	T-47D	breast:	n/a
36	chr3:101659630-101659680	CMK	blood:	n/a
37	chr3:101659630-101659680	BJ	skin:	n/a
38	chr3:101659630-101659680	Caco-2	colon:	n/a
39	chr3:101659630-101659680	PANC-1	pancreas:	n/a
40	chr3:101659630-101659680	HAEpiC	amniotic membrane:	n/a
41	chr3:101659630-101659680	Hela-S3	cervix:	n/a
42	chr3:101659630-101659680	AG10803	skin:	n/a
43	chr3:101659630-101659680	HRE	kidney:	n/a
44	chr3:101659630-101659680	PrEC	prostate:	n/a
45	chr3:101659630-101659680	HMEC	breast:	n/a
46	chr3:101659630-101659680	HCPEpiC	choroid plexus:	n/a
47	chr3:101659630-101659680	ovcar-3	ovarian:	n/a
48	chr3:101659630-101659680	SKMC	muscle:	n/a
49	chr3:101659630-101659680	GM06990	blood:	n/a
50	chr3:101659630-101659680	SK-N-SH_RA	brain:	n/a

Variant related genes	Relation type
ENSG00000214407	TF binding region
ENSG00000214407	CpG island

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1672376	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1672377	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1672379	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1672382	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1672384	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1707600	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1707610	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2925329	0.88[ASN][1000 genomes]
rs2942717	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2943301	0.87[ASW][hapmap];1.00[YRI][hapmap]
rs606407	0.82[ASN][1000 genomes]
rs635268	1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.84[YRI][hapmap]
rs796417	0.88[ASN][1000 genomes]
rs797867	0.87[ASN][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	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv3351469	chr3:101511702-101866448	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1010762	chr3:101584836-101803821	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101654000-101660200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr3:101654000-101661400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:101654000-101662800	Enhancers	Primary B cells from peripheral blood	blood
4	chr3:101654200-101662200	Enhancers	Primary T cells from cord blood	blood
5	chr3:101655400-101660000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr3:101655600-101660000	Enhancers	Hela-S3	cervix
7	chr3:101655600-101660600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:101656000-101661400	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr3:101656000-101661600	Enhancers	Fetal Heart	heart
10	chr3:101656000-101662400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:101656000-101662400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr3:101656200-101662800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr3:101657000-101661400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:101657400-101661200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:101657600-101660400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:101657600-101662400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:101657800-101661200	Enhancers	Primary B cells from cord blood	blood
18	chr3:101658200-101661400	Enhancers	NHEK	skin
19	chr3:101658400-101661400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr3:101658600-101660000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:101658600-101660000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:101658600-101660000	Flanking Active TSS	Fetal Lung	lung
23	chr3:101658600-101660000	Enhancers	Fetal Muscle Leg	muscle
24	chr3:101658600-101660400	Enhancers	Fetal Stomach	stomach
25	chr3:101658600-101661400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:101658800-101659800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:101658800-101660000	Enhancers	Colon Smooth Muscle	Colon
28	chr3:101658800-101660600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:101659000-101659800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr3:101659000-101660000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:101659000-101660000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:101659000-101660000	Flanking Active TSS	HUVEC	blood vessel
33	chr3:101659200-101659800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:101659200-101659800	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr3:101659200-101659800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr3:101659200-101659800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:101659200-101659800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:101659200-101659800	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr3:101659200-101659800	Active TSS	Stomach Smooth Muscle	stomach
40	chr3:101659200-101660000	Enhancers	Ovary	ovary
41	chr3:101659200-101660000	Flanking Active TSS	HMEC	breast
42	chr3:101659200-101660000	Flanking Active TSS	K562	blood
43	chr3:101659200-101660200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:101659400-101659800	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr3:101659400-101659800	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr3:101659400-101659800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr3:101659400-101659800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr3:101659400-101659800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:101659400-101659800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:101659400-101659800	Weak transcription	Placenta Amnion	Placenta Amnion

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