Variant report

Variant	rs11942648
Chromosome Location	chr4:126310893-126310894
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	TEAD4	chr4:126310744-126311500	SK-N-SH	brain:	n/a	n/a
2	PBX3	chr4:126310771-126311720	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr4:126310604-126312455	SK-N-SH	brain:	n/a	n/a
4	MAFK	chr4:126310859-126311582	IMR90	lung:	n/a	chr4:126311230-126311244
5	EP300	chr4:126310744-126311213	A549	lung:	n/a	chr4:126311082-126311091
6	JUND	chr4:126310840-126311270	MCF-7	breast:	n/a	chr4:126311082-126311092 chr4:126311081-126311092 chr4:126311082-126311092 chr4:126311083-126311092
7	STAT3	chr4:126310824-126311177	MCF10A-Er-Src	breast:	n/a	chr4:126311083-126311092
8	FOS	chr4:126310802-126311538	MCF10A-Er-Src	breast:	n/a	chr4:126311082-126311092 chr4:126311082-126311092 chr4:126311081-126311092 chr4:126311083-126311092
9	JUND	chr4:126310606-126311671	SK-N-SH	brain:	n/a	chr4:126311082-126311092 chr4:126311081-126311092 chr4:126311082-126311092 chr4:126311083-126311092
10	TEAD4	chr4:126310630-126311560	SK-N-SH	brain:	n/a	n/a
11	MYC	chr4:126310806-126311483	MCF10A-Er-Src	breast:	n/a	n/a
12	GATA3	chr4:126310800-126311157	T-47D	breast:	n/a	n/a
13	MEF2A	chr4:126310669-126311439	SK-N-SH	brain:	n/a	chr4:126310899-126310910 chr4:126310895-126310916 chr4:126311083-126311091 chr4:126310900-126310909 chr4:126310896-126310912 chr4:126310897-126310912
14	POLR2A	chr4:126310777-126311876	HUVEC	blood vessel:	n/a	n/a
15	FOSL2	chr4:126310772-126311208	A549	lung:	n/a	chr4:126311082-126311092 chr4:126311082-126311092 chr4:126311083-126311092
16	CEBPB	chr4:126310766-126311604	IMR90	lung:	n/a	chr4:126311362-126311371 chr4:126311362-126311371
17	GATA3	chr4:126310559-126312450	SK-N-SH	brain:	n/a	n/a
18	JUND	chr4:126310776-126311648	Hela-S3	cervix:	n/a	chr4:126311082-126311092 chr4:126311081-126311092 chr4:126311082-126311092 chr4:126311083-126311092
19	CEBPB	chr4:126310799-126311527	Hela-S3	cervix:	n/a	chr4:126311362-126311371 chr4:126311362-126311371
20	JUND	chr4:126310591-126312410	SK-N-SH	brain:	n/a	chr4:126311082-126311092 chr4:126311081-126311092 chr4:126311082-126311092 chr4:126311083-126311092
21	MEF2A	chr4:126310616-126311334	SK-N-SH	brain:	n/a	chr4:126310899-126310910 chr4:126310895-126310916 chr4:126311083-126311091 chr4:126310900-126310909 chr4:126310896-126310912 chr4:126310897-126310912
22	NFIC	chr4:126310771-126311330	ECC-1	luminal epithelium:	n/a	n/a
23	GATA3	chr4:126310808-126311162	T-47D	breast:	n/a	n/a
24	EP300	chr4:126310561-126311719	SK-N-SH	brain:	n/a	chr4:126311082-126311091
25	TEAD4	chr4:126310814-126311364	ECC-1	luminal epithelium:	n/a	n/a
26	NFIC	chr4:126310577-126312371	SK-N-SH	brain:	n/a	n/a
27	FOSL2	chr4:126310809-126311354	MCF-7	breast:	n/a	chr4:126311082-126311092 chr4:126311082-126311092 chr4:126311083-126311092
28	PBX3	chr4:126310669-126311744	SK-N-SH	brain:	n/a	n/a
29	NFIC	chr4:126310777-126311389	SK-N-SH	brain:	n/a	n/a
30	FOSL2	chr4:126310634-126312276	SK-N-SH	brain:	n/a	chr4:126311082-126311092 chr4:126311082-126311092 chr4:126311083-126311092
31	POLR2A	chr4:126310879-126311800	HUVEC	blood vessel:	n/a	n/a
32	STAT3	chr4:126310569-126311597	MCF10A-Er-Src	breast:	n/a	chr4:126311083-126311092 chr4:126311523-126311531 chr4:126311293-126311300
33	POLR2A	chr4:126310732-126311318	SK-N-SH	brain:	n/a	n/a
34	TCF7L2	chr4:126310855-126311213	PANC-1	pancreas:	n/a	chr4:126311083-126311092
35	JUND	chr4:126310682-126312353	SK-N-SH	brain:	n/a	chr4:126311082-126311092 chr4:126311081-126311092 chr4:126311082-126311092 chr4:126311083-126311092
36	NR3C1	chr4:126310821-126311152	A549	lung:	n/a	chr4:126311035-126311061 chr4:126311035-126311061
37	GATA3	chr4:126310588-126312492	SK-N-SH	brain:	n/a	n/a
38	FOS	chr4:126310569-126311594	MCF10A-Er-Src	breast:	n/a	chr4:126311082-126311092 chr4:126311082-126311092 chr4:126311081-126311092 chr4:126311083-126311092
39	GATA3	chr4:126310705-126311346	A549	lung:	n/a	n/a
40	FOS	chr4:126310891-126311492	MCF10A-Er-Src	breast:	n/a	chr4:126311082-126311092 chr4:126311082-126311092 chr4:126311081-126311092 chr4:126311083-126311092
41	FOS	chr4:126310776-126311607	MCF10A-Er-Src	breast:	n/a	chr4:126311082-126311092 chr4:126311082-126311092 chr4:126311081-126311092 chr4:126311083-126311092
42	EP300	chr4:126310620-126312354	SK-N-SH	brain:	n/a	chr4:126311082-126311091
43	FOS	chr4:126310823-126311681	HUVEC	blood vessel:	n/a	chr4:126311082-126311092 chr4:126311082-126311092 chr4:126311081-126311092 chr4:126311083-126311092
44	JUN	chr4:126310813-126311912	HUVEC	blood vessel:	n/a	chr4:126311082-126311092 chr4:126311082-126311092 chr4:126311083-126311092
45	TCF12	chr4:126310543-126311691	SK-N-SH	brain:	n/a	n/a
46	GATA3	chr4:126310623-126311435	MCF-7	breast:	n/a	n/a
47	MYC	chr4:126310836-126311516	MCF10A-Er-Src	breast:	n/a	n/a
48	TEAD4	chr4:126310790-126311318	ECC-1	luminal epithelium:	n/a	n/a
49	EP300	chr4:126310856-126311321	Hela-S3	cervix:	n/a	chr4:126311082-126311091
50	FOSL2	chr4:126310817-126311396	SK-N-SH	brain:	n/a	chr4:126311082-126311092 chr4:126311082-126311092 chr4:126311083-126311092

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:126235254..126237583-chr4:126309909..126311775,2	MCF-7	breast:

Variant related genes	Relation type
FAT4	TF binding region
ENSG00000196159	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10857105	0.81[AFR][1000 genomes]
rs11733424	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12711125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1396700	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1509288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1509293	0.81[AFR][1000 genomes]
rs1509294	0.81[AFR][1000 genomes]
rs1509295	0.81[AFR][1000 genomes]
rs1509296	0.81[AFR][1000 genomes]
rs1509297	0.81[AFR][1000 genomes]
rs1509298	0.81[AFR][1000 genomes]
rs1509301	0.81[AFR][1000 genomes]
rs1605825	0.81[AFR][1000 genomes]
rs1605826	0.81[AFR][1000 genomes]
rs1605827	0.81[AFR][1000 genomes]
rs2055768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2102461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2457262	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2663253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2663258	1.00[AMR][1000 genomes]
rs2663262	1.00[AMR][1000 genomes]
rs2663284	1.00[AMR][1000 genomes]
rs2710537	1.00[AMR][1000 genomes]
rs2710565	1.00[AMR][1000 genomes]
rs2710577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2710581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2710585	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2710586	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2710588	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28470542	1.00[AMR][1000 genomes]
rs28871071	1.00[AMR][1000 genomes]
rs4834029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6844307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7660088	0.81[AFR][1000 genomes]
rs7660325	0.81[AFR][1000 genomes]
rs906793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs906794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs925244	1.00[AMR][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	nsv1006068	chr4:126103233-126497467	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv830051	chr4:126234895-126403426	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv470070	chr4:126299145-126408586	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:126290800-126317600	Weak transcription	Fetal Brain Male	brain
2	chr4:126296000-126311200	Weak transcription	Aorta	Aorta
3	chr4:126308400-126336000	Weak transcription	Left Ventricle	heart
4	chr4:126308600-126311000	Enhancers	Osteobl	bone
5	chr4:126308800-126311200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:126308800-126311200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:126309000-126311200	Enhancers	NHDF-Ad	bronchial
8	chr4:126309000-126311400	Enhancers	NHLF	lung
9	chr4:126309000-126312000	Enhancers	Colon Smooth Muscle	Colon
10	chr4:126309200-126311000	Enhancers	Adipose Nuclei	Adipose
11	chr4:126309200-126311200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:126309200-126311200	Enhancers	HSMMtube	muscle
13	chr4:126309200-126311400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:126309200-126311400	Weak transcription	Brain Substantia Nigra	brain
15	chr4:126309200-126312000	Enhancers	Rectal Smooth Muscle	rectum
16	chr4:126309400-126311200	Enhancers	NH-A	brain
17	chr4:126309400-126311400	Weak transcription	Fetal Stomach	stomach
18	chr4:126309600-126311000	Enhancers	Fetal Heart	heart
19	chr4:126309800-126311800	Enhancers	Fetal Lung	lung
20	chr4:126309800-126312000	Enhancers	HMEC	breast
21	chr4:126309800-126312000	Enhancers	NHEK	skin
22	chr4:126309800-126312200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:126310000-126312000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:126310200-126311000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr4:126310200-126311200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:126310200-126311400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:126310600-126311200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:126310600-126311600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:126310600-126311600	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr4:126310600-126311800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:126310800-126311000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:126310800-126311200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr4:126310800-126311200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr4:126310800-126311200	Enhancers	HSMM	muscle
35	chr4:126310800-126311200	Enhancers	HUVEC	blood vessel
36	chr4:126310800-126311400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:126310800-126311400	Enhancers	Brain Angular Gyrus	brain
38	chr4:126310800-126311400	Active TSS	A549	lung
39	chr4:126310800-126311600	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr4:126310800-126311800	Enhancers	Hela-S3	cervix
41	chr4:126310800-126317200	Weak transcription	Fetal Kidney	kidney
42	chr4:126310800-126336000	Weak transcription	Fetal Muscle Trunk	muscle

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