Variant report

Variant	rs1319101
Chromosome Location	chr3:143569790-143569791
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	MYC	chr3:143569714-143569999	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr3:143569691-143570020	MCF10A-Er-Src	breast:	n/a	n/a
3	ATF2	chr3:143569668-143570218	GM12878	blood:	n/a	n/a
4	BATF	chr3:143569705-143570077	GM12878	blood:	n/a	n/a
5	MYC	chr3:143569708-143569933	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr3:143569744-143570040	MCF10A-Er-Src	breast:	n/a	n/a
7	RELA	chr3:143569703-143570265	GM12878	blood:	n/a	n/a
8	RUNX3	chr3:143569777-143570186	GM12878	blood:	n/a	n/a
9	RELA	chr3:143569765-143570166	GM10847	blood:	n/a	n/a
10	NFIC	chr3:143569662-143570236	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:143569538-143569897	MCF10A-Er-Src	breast:	n/a	n/a
12	RELA	chr3:143569727-143570483	GM18951	blood:	n/a	n/a
13	FOS	chr3:143569665-143570107	MCF10A-Er-Src	breast:	n/a	n/a
14	BCL11A	chr3:143569728-143570094	GM12878	blood:	n/a	n/a
15	RELA	chr3:143569783-143570123	GM15510	blood:	n/a	n/a
16	RELA	chr3:143569398-143570614	GM12891	blood:	n/a	n/a
17	STAT3	chr3:143569704-143569989	MCF10A-Er-Src	breast:	n/a	n/a
18	FOS	chr3:143569665-143570437	MCF10A-Er-Src	breast:	n/a	chr3:143570263-143570275
19	RELA	chr3:143569729-143570656	GM19099	blood:	n/a	n/a
20	FOS	chr3:143569707-143569956	MCF10A-Er-Src	breast:	n/a	n/a
21	RELA	chr3:143569731-143570310	GM18505	blood:	n/a	n/a

Variant related genes	Relation type
SLC9A9	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10433436	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11714060	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1319100	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1394398	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1394402	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1900644	1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs1979911	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1995529	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1995530	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2011290	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2361202	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2361203	0.94[EUR][1000 genomes]
rs2361205	0.94[EUR][1000 genomes]
rs2361206	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2361207	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2361208	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2361209	1.00[EUR][1000 genomes]
rs2885193	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2885194	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2885195	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4286430	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4499594	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4593022	0.84[AMR][1000 genomes]
rs4839612	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4839671	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4839672	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4839673	1.00[EUR][1000 genomes]
rs4839674	1.00[CEU][hapmap]
rs6440195	1.00[CEU][hapmap]
rs6440196	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6768702	1.00[EUR][1000 genomes]
rs6773087	0.84[AMR][1000 genomes]
rs6780027	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6782974	1.00[CEU][hapmap]
rs7623477	1.00[EUR][1000 genomes]
rs7627020	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7629598	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7645681	1.00[EUR][1000 genomes]
rs9289669	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9824974	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9836851	1.00[EUR][1000 genomes]
rs9870661	1.00[CEU][hapmap];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
rs1319101	C14orf143	trans	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143567400-143570000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr3:143567400-143570600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:143567400-143571000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:143567800-143569800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:143567800-143569800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:143567800-143570000	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr3:143567800-143570000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:143567800-143570200	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:143567800-143570400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:143567800-143571000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:143568000-143569800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:143568400-143570000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:143568400-143570400	Flanking Active TSS	GM12878-XiMat	blood
14	chr3:143568400-143570600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:143568600-143569800	Enhancers	Primary B cells from cord blood	blood
16	chr3:143568600-143570400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:143568600-143571000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:143568800-143569800	Weak transcription	Osteobl	bone
19	chr3:143568800-143570200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:143568800-143570600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr3:143569000-143570800	Flanking Active TSS	NHEK	skin
22	chr3:143569200-143570200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr3:143569200-143570400	Enhancers	NHDF-Ad	bronchial
24	chr3:143569200-143573000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:143569200-143573800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr3:143569400-143570400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:143569400-143571000	Enhancers	HMEC	breast
28	chr3:143569400-143573200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr3:143569600-143570000	Weak transcription	Fetal Thymus	thymus
30	chr3:143569600-143570000	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr3:143569600-143570400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:143569600-143570400	Enhancers	NHLF	lung
33	chr3:143569600-143570600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:143569600-143572600	Weak transcription	Primary T cells from cord blood	blood
35	chr3:143569600-143572800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:143569600-143573200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:143569600-143574000	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr3:143569600-143574000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr3:143569600-143574000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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