Variant report

Variant	rs59944801
Chromosome Location	chr4:152149347-152149348
allele	C/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	FOS	chr4:152148811-152149447	HUVEC	blood vessel:	n/a	chr4:152149115-152149124
2	POLR2A	chr4:152147209-152150071	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr4:152148688-152149403	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr4:152148660-152149481	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr4:152148535-152149562	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr4:152148659-152149922	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr4:152148636-152149374	MCF10A-Er-Src	breast:	n/a	chr4:152148669-152148681 chr4:152149115-152149124
8	POLR2A	chr4:152148681-152149479	IMR90	lung:	n/a	n/a
9	JUN	chr4:152148768-152149434	HUVEC	blood vessel:	n/a	chr4:152149115-152149124
10	FOS	chr4:152148751-152149486	MCF10A-Er-Src	breast:	n/a	chr4:152149115-152149124
11	STAT3	chr4:152149256-152149384	MCF10A-Er-Src	breast:	n/a	n/a
12	TEAD4	chr4:152148893-152149456	ECC-1	luminal epithelium:	n/a	chr4:152149151-152149160
13	STAT3	chr4:152148910-152149446	MCF10A-Er-Src	breast:	n/a	n/a
14	E2F4	chr4:152148989-152149442	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
SH3D19	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12503016	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12504166	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12508270	0.82[ASN][1000 genomes]
rs12510153	0.83[ASN][1000 genomes]
rs12511209	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17633530	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17633537	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17633600	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17633648	0.99[ASN][1000 genomes]
rs17633654	0.99[ASN][1000 genomes]
rs2407420	0.87[EUR][1000 genomes]
rs58496896	0.92[ASN][1000 genomes]
rs60212468	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60367453	0.91[ASN][1000 genomes]
rs60761330	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72967545	0.99[ASN][1000 genomes]
rs7671332	0.99[ASN][1000 genomes]
rs7699574	0.88[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	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv948719	chr4:151693149-152161625	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1016220	chr4:151997139-152164126	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv537306	chr4:151997139-152164126	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv870229	chr4:152114410-152161072	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152120800-152153800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:152129000-152168000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:152129400-152167800	Weak transcription	Right Ventricle	heart
4	chr4:152130200-152187800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr4:152136600-152158000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:152141000-152167400	Weak transcription	HepG2	liver
7	chr4:152144800-152163400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:152145800-152149600	Active TSS	Right Atrium	heart
9	chr4:152146000-152149400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:152146200-152149800	Flanking Active TSS	HUVEC	blood vessel
11	chr4:152146600-152149600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:152147000-152149400	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr4:152147200-152149400	Active TSS	Brain Hippocampus Middle	brain
14	chr4:152147200-152150200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr4:152147200-152150200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr4:152147200-152160200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:152147400-152149600	Active TSS	Aorta	Aorta
18	chr4:152147400-152149600	Enhancers	Colon Smooth Muscle	Colon
19	chr4:152147400-152150200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:152147600-152149800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:152147600-152150200	Enhancers	Fetal Heart	heart
22	chr4:152147600-152150800	Enhancers	Fetal Stomach	stomach
23	chr4:152148000-152149600	Enhancers	HSMM	muscle
24	chr4:152148000-152158000	Weak transcription	Fetal Intestine Small	intestine
25	chr4:152148000-152164200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:152148200-152150000	Enhancers	A549	lung
27	chr4:152148200-152158200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:152148200-152163400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr4:152148400-152149600	Flanking Active TSS	Fetal Lung	lung
30	chr4:152148600-152149600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr4:152148600-152149600	Flanking Active TSS	Osteobl	bone
32	chr4:152148800-152149400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:152148800-152149400	Flanking Active TSS	NHEK	skin
34	chr4:152148800-152149600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr4:152148800-152149800	Enhancers	Liver	Liver
36	chr4:152148800-152153200	Weak transcription	Lung	lung
37	chr4:152149000-152149400	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr4:152149000-152149600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:152149000-152149600	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr4:152149000-152150200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:152149200-152149400	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr4:152149200-152149400	Active TSS	Adipose Nuclei	Adipose
43	chr4:152149200-152149400	Active TSS	Stomach Smooth Muscle	stomach
44	chr4:152149200-152149400	Active TSS	NHDF-Ad	bronchial
45	chr4:152149200-152149600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:152149200-152149600	Flanking Active TSS	Brain Angular Gyrus	brain
47	chr4:152149200-152149600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr4:152149200-152149600	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr4:152149200-152149600	Enhancers	Placenta Amnion	Placenta Amnion
50	chr4:152149200-152149600	Enhancers	Rectal Smooth Muscle	rectum

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