Variant report

Variant	rs2361209
Chromosome Location	chr3:143568783-143568784
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	MEF2A	chr3:143568736-143569109	GM12878	blood:	n/a	chr3:143568826-143568834
2	CEBPB	chr3:143568679-143569247	IMR90	lung:	n/a	n/a
3	RUNX3	chr3:143568703-143569023	GM12878	blood:	n/a	n/a
4	BATF	chr3:143568675-143569126	GM12878	blood:	n/a	chr3:143569072-143569081 chr3:143568916-143568927
5	POLR2A	chr3:143568777-143569112	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr3:143568734-143569119	HUVEC	blood vessel:	n/a	chr3:143568918-143568929
7	FOS	chr3:143568712-143569245	MCF10A-Er-Src	breast:	n/a	chr3:143568918-143568929
8	BATF	chr3:143568766-143569102	GM12878	blood:	n/a	chr3:143569072-143569081 chr3:143568916-143568927
9	FOS	chr3:143568627-143569267	MCF10A-Er-Src	breast:	n/a	chr3:143568631-143568643 chr3:143568918-143568929
10	MAFK	chr3:143568705-143568869	HepG2	liver:	n/a	chr3:143568785-143568801 chr3:143568783-143568803 chr3:143568786-143568800
11	MYC	chr3:143568644-143569203	MCF10A-Er-Src	breast:	n/a	n/a
12	STAT3	chr3:143568740-143569149	MCF10A-Er-Src	breast:	n/a	n/a
13	ATF2	chr3:143568557-143569164	GM12878	blood:	n/a	n/a
14	STAT3	chr3:143568640-143569188	MCF10A-Er-Src	breast:	n/a	n/a
15	EBF1	chr3:143568756-143568990	GM12878	blood:	n/a	n/a
16	FOXM1	chr3:143568582-143569234	GM12878	blood:	n/a	n/a
17	FOXM1	chr3:143568625-143569159	GM12878	blood:	n/a	n/a
18	MYC	chr3:143568660-143569147	MCF10A-Er-Src	breast:	n/a	n/a
19	STAT3	chr3:143568706-143569158	MCF10A-Er-Src	breast:	n/a	n/a
20	FOS	chr3:143568659-143569186	MCF10A-Er-Src	breast:	n/a	chr3:143568918-143568929
21	NFIC	chr3:143568593-143569221	GM12878	blood:	n/a	n/a
22	BCL11A	chr3:143568715-143569009	GM12878	blood:	n/a	n/a
23	RUNX3	chr3:143568618-143569310	GM12878	blood:	n/a	n/a
24	NFIC	chr3:143568637-143569194	GM12878	blood:	n/a	n/a
25	STAT3	chr3:143568706-143569127	MCF10A-Er-Src	breast:	n/a	n/a
26	BCLAF1	chr3:143568692-143569195	GM12878	blood:	n/a	n/a
27	FOS	chr3:143568713-143569183	MCF10A-Er-Src	breast:	n/a	chr3:143568918-143568929
28	MAFK	chr3:143568590-143569002	IMR90	lung:	n/a	chr3:143568785-143568801 chr3:143568783-143568803 chr3:143568786-143568800
29	MTA3	chr3:143568575-143569177	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143566553..143569042-chr3:143690803..143692633,2	MCF-7	breast:

Variant related genes	Relation type
SLC9A9	TF binding region
ENSG00000181744	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10433436	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11714060	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1319100	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1319101	1.00[EUR][1000 genomes]
rs1394398	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1394402	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1979911	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1995529	1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1995530	1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2011290	1.00[EUR][1000 genomes]
rs2361202	1.00[EUR][1000 genomes]
rs2361203	0.94[EUR][1000 genomes]
rs2361205	0.94[EUR][1000 genomes]
rs2361206	0.94[EUR][1000 genomes]
rs2361207	0.84[ASW][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs2361208	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2885193	0.94[EUR][1000 genomes]
rs2885194	0.94[EUR][1000 genomes]
rs2885195	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4286430	1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs4499594	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4839612	0.94[EUR][1000 genomes]
rs4839671	1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs4839672	0.94[EUR][1000 genomes]
rs4839673	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4839674	1.00[CEU][hapmap]
rs6440196	1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs6768702	1.00[EUR][1000 genomes]
rs6780027	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6782974	1.00[TSI][hapmap]
rs7623477	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7627020	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7629598	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7645681	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9289669	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9822158	1.00[MEX][hapmap]
rs9824974	1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9836851	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9841753	1.00[MEX][hapmap]
rs9870661	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2361209	C14orf143	trans	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143565800-143569200	Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr3:143567400-143568800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:143567400-143569000	Enhancers	HSMM	muscle
4	chr3:143567400-143569000	Enhancers	NHEK	skin
5	chr3:143567400-143570000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr3:143567400-143570600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:143567400-143571000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:143567600-143569000	Enhancers	HMEC	breast
9	chr3:143567600-143569200	Enhancers	Fetal Stomach	stomach
10	chr3:143567600-143569200	Enhancers	HUVEC	blood vessel
11	chr3:143567600-143569400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr3:143567600-143569600	Enhancers	Primary T cells from cord blood	blood
13	chr3:143567600-143569600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:143567600-143569600	Enhancers	HSMMtube	muscle
15	chr3:143567800-143568800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:143567800-143568800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:143567800-143568800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:143567800-143568800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:143567800-143569000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:143567800-143569000	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr3:143567800-143569000	Enhancers	NHLF	lung
22	chr3:143567800-143569200	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr3:143567800-143569200	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr3:143567800-143569200	Enhancers	NH-A	brain
25	chr3:143567800-143569400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:143567800-143569600	Enhancers	Primary T cells fromperipheralblood	blood
27	chr3:143567800-143569600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:143567800-143569600	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr3:143567800-143569600	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr3:143567800-143569600	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr3:143567800-143569800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:143567800-143569800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:143567800-143570000	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr3:143567800-143570000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:143567800-143570200	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:143567800-143570400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:143567800-143571000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:143568000-143568800	Flanking Active TSS	NHDF-Ad	bronchial
39	chr3:143568000-143569600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr3:143568000-143569800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr3:143568400-143568800	Weak transcription	Adipose Nuclei	Adipose
42	chr3:143568400-143568800	Enhancers	Rectal Smooth Muscle	rectum
43	chr3:143568400-143569000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:143568400-143569200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:143568400-143569200	Enhancers	Brain Angular Gyrus	brain
46	chr3:143568400-143569400	Weak transcription	Fetal Thymus	thymus
47	chr3:143568400-143569600	Enhancers	Brain Hippocampus Middle	brain
48	chr3:143568400-143569600	Enhancers	Brain Substantia Nigra	brain
49	chr3:143568400-143570000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:143568400-143570400	Flanking Active TSS	GM12878-XiMat	blood

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