Variant report

Variant	rs73830477
Chromosome Location	chr3:48733134-48733135
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	JUND	chr3:48732803-48733197	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:48732650-48733169	HUVEC	blood vessel:	n/a	n/a
3	MYC	chr3:48732918-48733145	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr3:48732152-48733157	GM12892	blood:	n/a	n/a
5	POLR2A	chr3:48732111-48733278	H1-hESC	embryonic stem cell:	n/a	n/a
6	JUN	chr3:48732878-48733167	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:48732303-48733134	A549	lung:	n/a	n/a
8	POLR2A	chr3:48732215-48733242	GM12891	blood:	n/a	n/a
9	FOXP2	chr3:48732706-48733136	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr3:48731964-48733172	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:48732380-48733201	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:48731983-48733135	U87	brain:	n/a	n/a
13	ATF2	chr3:48732618-48733242	H1-hESC	embryonic stem cell:	n/a	n/a
14	MYC	chr3:48732888-48733138	H1-hESC	embryonic stem cell:	n/a	n/a
15	GTF2F1	chr3:48732797-48733135	H1-hESC	embryonic stem cell:	n/a	n/a
16	SP1	chr3:48732875-48733215	H1-hESC	embryonic stem cell:	n/a	chr3:48733041-48733050 chr3:48733039-48733051 chr3:48732996-48733007 chr3:48733039-48733051 chr3:48733040-48733050 chr3:48733040-48733049 chr3:48733039-48733050 chr3:48733041-48733050
17	POLR2A	chr3:48732083-48733179	GM12878	blood:	n/a	n/a
18	ATF2	chr3:48732554-48733226	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr3:48732074-48733145	HepG2	liver:	n/a	n/a
20	MAZ	chr3:48731099-48733260	IMR90	lung:	n/a	n/a
21	POLR2A	chr3:48732282-48733231	H1-hESC	embryonic stem cell:	n/a	n/a
22	TAF1	chr3:48732610-48733182	H1-hESC	embryonic stem cell:	n/a	n/a
23	STAT3	chr3:48733020-48733222	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr3:48732336-48733227	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48699225..48701604-chr3:48731929..48734312,2	MCF-7	breast:
2	chr3:48732542..48735376-chr3:48750993..48752883,2	K562	blood:
3	chr3:48730035..48731678-chr3:48732538..48734765,2	MCF-7	breast:

Variant related genes	Relation type
IP6K2	TF binding region
ENSG00000068745	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000228350	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs56204480	0.92[AFR][1000 genomes]
rs57555186	1.00[AMR][1000 genomes]
rs60636203	1.00[AMR][1000 genomes]
rs73830470	1.00[AMR][1000 genomes]
rs73830472	1.00[AMR][1000 genomes]
rs73830473	1.00[AMR][1000 genomes]
rs73830476	0.81[AFR][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	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48723800-48733800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:48724400-48735800	Strong transcription	GM12878-XiMat	blood
3	chr3:48724600-48734000	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr3:48724600-48734000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:48724600-48738000	Strong transcription	Thymus	Thymus
6	chr3:48724600-48738400	Strong transcription	Primary hematopoietic stem cells	blood
7	chr3:48724600-48740400	Strong transcription	Primary B cells from cord blood	blood
8	chr3:48724600-48746600	Strong transcription	Fetal Thymus	thymus
9	chr3:48724600-48749000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:48724800-48733800	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr3:48724800-48733800	Strong transcription	HepG2	liver
12	chr3:48724800-48734000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:48724800-48735800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:48724800-48737600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:48724800-48738400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr3:48725000-48733200	Strong transcription	Liver	Liver
17	chr3:48725000-48738600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr3:48725000-48738600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:48725000-48740400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:48725000-48740800	Strong transcription	Dnd41	blood
21	chr3:48725200-48733200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:48725200-48738600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr3:48725200-48746200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:48725400-48733200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:48730600-48733600	Weak transcription	K562	blood
26	chr3:48731000-48733200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:48731000-48733200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:48731000-48733200	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
29	chr3:48731000-48734000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:48731200-48735000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:48731400-48733200	Flanking Active TSS	NH-A	brain
32	chr3:48731400-48733200	Transcr. at gene 5' and 3'	Osteobl	bone
33	chr3:48731400-48734400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr3:48731600-48733200	Genic enhancers	Fetal Muscle Trunk	muscle
35	chr3:48731800-48733800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:48732000-48733200	Genic enhancers	Fetal Lung	lung
37	chr3:48732000-48733200	Transcr. at gene 5' and 3'	HMEC	breast
38	chr3:48732000-48734400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:48732000-48734400	Genic enhancers	A549	lung
40	chr3:48732200-48733200	Flanking Active TSS	Brain Angular Gyrus	brain
41	chr3:48732200-48733200	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr3:48732200-48733200	Flanking Active TSS	Brain Cingulate Gyrus	brain
43	chr3:48732200-48733200	Flanking Active TSS	Brain Substantia Nigra	brain
44	chr3:48732200-48734400	Genic enhancers	Fetal Kidney	kidney
45	chr3:48732200-48735200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:48732400-48733200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:48732400-48733200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:48732400-48733200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
49	chr3:48732400-48733200	Genic enhancers	Fetal Intestine Small	intestine
50	chr3:48732400-48733200	Genic enhancers	Placenta	Placenta

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