Variant report

Variant	rs3755721
Chromosome Location	chr3:69131592-69131593
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	TCF12	chr3:69130875-69131640	SK-N-SH	brain:	n/a	chr3:69131325-69131333
2	STAT3	chr3:69131165-69132470	MCF10A-Er-Src	breast:	n/a	chr3:69131735-69131744 chr3:69132200-69132207 chr3:69131661-69131673 chr3:69131736-69131745
3	NFIC	chr3:69131523-69132588	GM12878	blood:	n/a	n/a
4	FOS	chr3:69131060-69132333	MCF10A-Er-Src	breast:	n/a	chr3:69131736-69131743 chr3:69131735-69131744 chr3:69131736-69131744 chr3:69131232-69131243 chr3:69131735-69131745 chr3:69131234-69131242
5	POLR2A	chr3:69128206-69135962	GM12878	blood:	n/a	n/a
6	EBF1	chr3:69131435-69132761	GM12878	blood:	n/a	chr3:69132172-69132183
7	GATA3	chr3:69130776-69131751	SK-N-SH	brain:	n/a	n/a
8	EP300	chr3:69130718-69132499	SK-N-SH	brain:	n/a	chr3:69131735-69131744 chr3:69131736-69131745
9	FOS	chr3:69130973-69131929	HUVEC	blood vessel:	n/a	chr3:69131736-69131743 chr3:69131735-69131744 chr3:69131736-69131744 chr3:69131232-69131243 chr3:69131735-69131745 chr3:69131234-69131242
10	GATA1	chr3:69130254-69131852	PBDE	blood:	n/a	n/a
11	STAT3	chr3:69131167-69132613	MCF10A-Er-Src	breast:	n/a	chr3:69131735-69131744 chr3:69132200-69132207 chr3:69131661-69131673 chr3:69131736-69131745
12	STAT3	chr3:69131196-69132575	MCF10A-Er-Src	breast:	n/a	chr3:69131735-69131744 chr3:69132200-69132207 chr3:69131661-69131673 chr3:69131736-69131745
13	GATA3	chr3:69130880-69131661	SK-N-SH	brain:	n/a	n/a
14	FOS	chr3:69131086-69132358	MCF10A-Er-Src	breast:	n/a	chr3:69131736-69131743 chr3:69131735-69131744 chr3:69131736-69131744 chr3:69131232-69131243 chr3:69131735-69131745 chr3:69131234-69131242
15	ZNF263	chr3:69130983-69131684	HEK293-T-REx	kidney:	n/a	n/a
16	JUND	chr3:69130819-69131599	SK-N-SH	brain:	n/a	chr3:69130908-69130919 chr3:69131234-69131242
17	MTA3	chr3:69130763-69131615	GM12878	blood:	n/a	n/a
18	FOS	chr3:69131122-69132253	MCF10A-Er-Src	breast:	n/a	chr3:69131736-69131743 chr3:69131735-69131744 chr3:69131736-69131744 chr3:69131232-69131243 chr3:69131735-69131745 chr3:69131234-69131242
19	TCF12	chr3:69130842-69131658	SK-N-SH	brain:	n/a	chr3:69131325-69131333
20	PBX3	chr3:69130995-69131596	SK-N-SH	brain:	n/a	chr3:69131289-69131300
21	POLR2A	chr3:69130649-69132842	GM12891	blood:	n/a	n/a
22	STAT3	chr3:69131168-69132288	MCF10A-Er-Src	breast:	n/a	chr3:69131735-69131744 chr3:69132200-69132207 chr3:69131661-69131673 chr3:69131736-69131745
23	PBX3	chr3:69130999-69131647	SK-N-SH	brain:	n/a	chr3:69131289-69131300

No.	Distal block	Cell Line	Cell type
1	chr3:69129691..69132145-chr3:69248056..69250822,2	MCF-7	breast:
2	chr3:69099731..69103494-chr3:69131306..69136379,6	MCF-7	breast:
3	chr3:69061476..69064768-chr3:69131300..69135318,3	K562	blood:
4	chr3:69128084..69131909-chr3:69132505..69136999,7	K562	blood:
5	chr3:69061713..69064386-chr3:69131300..69133862,4	K562	blood:

Variant related genes	Relation type
UBA3	TF binding region
ARL6IP5	TF binding region
ENSG00000144747	Chromatin interaction
ENSG00000163378	Chromatin interaction
ENSG00000114541	Chromatin interaction
ENSG00000244513	Chromatin interaction
ENSG00000144746	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2009602	0.81[ASN][1000 genomes]
rs2292198	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35718539	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3755717	0.85[AFR][1000 genomes]
rs3772979	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs3821562	0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs3853157	0.80[ASN][1000 genomes]
rs56156415	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs58950441	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6549181	0.86[AFR][1000 genomes]
rs6775065	0.81[ASN][1000 genomes]
rs6775256	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777032	0.80[ASN][1000 genomes]
rs6787569	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs714300	0.81[ASN][1000 genomes]
rs7615341	0.81[ASN][1000 genomes]
rs9813514	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876933	chr3:69059023-69227379	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv876934	chr3:69111512-69166895	Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69129400-69133400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:69129400-69133400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:69129400-69134000	Weak transcription	Gastric	stomach
4	chr3:69129600-69133200	Enhancers	Hela-S3	cervix
5	chr3:69129600-69133400	Weak transcription	Esophagus	oesophagus
6	chr3:69129600-69133400	Weak transcription	Pancreas	Pancrea
7	chr3:69129600-69133600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:69129600-69133600	Weak transcription	Right Ventricle	heart
9	chr3:69129600-69134000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:69129600-69134000	Enhancers	Small Intestine	intestine
11	chr3:69129800-69131800	Enhancers	Primary hematopoietic stem cells	blood
12	chr3:69129800-69132000	Enhancers	Primary T cells from cord blood	blood
13	chr3:69129800-69132000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:69129800-69133200	Enhancers	Fetal Heart	heart
15	chr3:69129800-69133200	Enhancers	HMEC	breast
16	chr3:69129800-69133400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:69129800-69133400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr3:69129800-69133400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:69130000-69131600	Enhancers	Brain Hippocampus Middle	brain
20	chr3:69130000-69131800	Weak transcription	Adipose Nuclei	Adipose
21	chr3:69130000-69131800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:69130000-69131800	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr3:69130000-69131800	Enhancers	NHLF	lung
24	chr3:69130000-69132000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:69130000-69132000	Enhancers	Primary B cells from peripheral blood	blood
26	chr3:69130000-69132000	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr3:69130000-69132000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:69130000-69132000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr3:69130000-69132000	Weak transcription	Brain Anterior Caudate	brain
30	chr3:69130000-69132000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr3:69130000-69132000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr3:69130000-69132000	Enhancers	Dnd41	blood
33	chr3:69130000-69132400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:69130000-69132600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:69130000-69132800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr3:69130000-69133000	Weak transcription	Liver	Liver
37	chr3:69130000-69133200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:69130000-69133200	Weak transcription	Colonic Mucosa	Colon
39	chr3:69130000-69133200	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr3:69130000-69133200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr3:69130000-69133200	Enhancers	HUVEC	blood vessel
42	chr3:69130000-69133400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr3:69130000-69133400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:69130000-69133400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr3:69130000-69133400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr3:69130000-69133400	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr3:69130000-69133400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:69130000-69133400	Enhancers	Brain Angular Gyrus	brain
49	chr3:69130000-69133400	Weak transcription	Brain Germinal Matrix	brain
50	chr3:69130000-69133400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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