Variant report

Variant	rs4407373
Chromosome Location	chr3:139255012-139255013
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	MXI1	chr3:139254870-139260531	SK-N-SH	brain:	n/a	n/a
2	EP300	chr3:139251629-139259175	SK-N-SH	brain:	n/a	chr3:139256357-139256366 chr3:139253631-139253641 chr3:139252024-139252040 chr3:139256356-139256365

No.	Distal block	Cell Line	Cell type
1	chr3:139253381..139256319-chr3:139269568..139271702,2	MCF-7	breast:
2	chr3:139239944..139241919-chr3:139253042..139255747,2	MCF-7	breast:
3	chr3:139251496..139253555-chr3:139254279..139256942,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248932	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1116748	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11549984	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485273	0.84[CEU][hapmap]
rs12489687	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695698	0.80[YRI][hapmap]
rs1391029	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1391030	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1391031	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511571	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17337746	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17397112	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011770	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2233811	0.81[YRI][hapmap]
rs2233815	0.81[YRI][hapmap]
rs3772868	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs3772878	0.81[YRI][hapmap]
rs3821543	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs3821544	0.80[YRI][hapmap]
rs4270469	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683502	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs55641400	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55642746	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55724241	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55780517	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55817881	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55834130	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55968289	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55987999	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56034427	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56051054	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56051514	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56058641	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56170893	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56210757	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56343214	0.92[EUR][1000 genomes]
rs57459746	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220932	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220940	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220941	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220944	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220945	0.97[ASN][1000 genomes]
rs893703	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9289576	0.81[YRI][hapmap]
rs9289578	0.81[YRI][hapmap]
rs930412	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831108	0.92[YRI][hapmap]
rs9834607	0.81[YRI][hapmap]
rs9835241	0.81[YRI][hapmap]
rs9849578	0.87[YRI][hapmap]
rs9860201	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer 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	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139249600-139256400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:139249800-139257400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:139250000-139256600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr3:139250600-139255400	Enhancers	Brain Angular Gyrus	brain
5	chr3:139250600-139256800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:139250800-139257400	Enhancers	Brain Cingulate Gyrus	brain
7	chr3:139251000-139255800	Enhancers	Fetal Kidney	kidney
8	chr3:139251200-139255800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:139251200-139257400	Genic enhancers	Fetal Intestine Small	intestine
10	chr3:139251400-139255400	Enhancers	Placenta	Placenta
11	chr3:139251400-139256400	Enhancers	Liver	Liver
12	chr3:139251400-139257200	Enhancers	Duodenum Mucosa	Duodenum
13	chr3:139251600-139255800	Enhancers	Fetal Brain Male	brain
14	chr3:139251600-139256400	Enhancers	HMEC	breast
15	chr3:139251800-139255200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:139251800-139258600	Enhancers	Fetal Heart	heart
17	chr3:139252000-139257600	Enhancers	Left Ventricle	heart
18	chr3:139252200-139257600	Enhancers	Brain Substantia Nigra	brain
19	chr3:139252400-139256200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:139252600-139255200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:139252600-139255200	Enhancers	Lung	lung
22	chr3:139252600-139255800	Enhancers	Right Atrium	heart
23	chr3:139252800-139255800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr3:139252800-139257600	Enhancers	Right Ventricle	heart
25	chr3:139252800-139257800	Weak transcription	Psoas Muscle	Psoas
26	chr3:139253000-139255400	Enhancers	Colonic Mucosa	Colon
27	chr3:139253000-139255400	Enhancers	Colon Smooth Muscle	Colon
28	chr3:139253000-139258000	Weak transcription	Small Intestine	intestine
29	chr3:139253000-139258200	Enhancers	Spleen	Spleen
30	chr3:139253400-139255400	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr3:139253400-139257400	Genic enhancers	Fetal Stomach	stomach
32	chr3:139253600-139257400	Enhancers	Brain Hippocampus Middle	brain
33	chr3:139253800-139255200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:139253800-139255200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:139253800-139256000	Enhancers	HSMMtube	muscle
36	chr3:139253800-139256400	Enhancers	NHEK	skin
37	chr3:139253800-139256600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:139253800-139257600	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr3:139254200-139255200	Enhancers	Hela-S3	cervix
40	chr3:139254200-139255800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:139254400-139255400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:139254400-139255400	Enhancers	Aorta	Aorta
43	chr3:139254400-139255400	Enhancers	Rectal Smooth Muscle	rectum
44	chr3:139254400-139255600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:139254400-139255600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:139254400-139255800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr3:139254400-139256400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr3:139254400-139256800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:139254600-139255200	Weak transcription	Fetal Intestine Large	intestine
50	chr3:139254600-139255400	Genic enhancers	Ovary	ovary

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