Variant report

Variant	rs17349579
Chromosome Location	chr1:169332898-169332899
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	CEBPB	chr1:169332550-169333212	Hela-S3	cervix:	n/a	n/a
2	RCOR1	chr1:169332062-169333086	IMR90	lung:	n/a	n/a
3	JUND	chr1:169332581-169332930	K562	blood:	n/a	chr1:169332734-169332745
4	JUND	chr1:169332212-169333088	SK-N-SH	brain:	n/a	chr1:169332734-169332745
5	MEF2A	chr1:169332495-169333023	GM12878	blood:	n/a	n/a
6	JUND	chr1:169332270-169332971	Hela-S3	cervix:	n/a	chr1:169332734-169332745
7	FOSL1	chr1:169332354-169332979	HCT-116	colon:	n/a	n/a
8	MTA3	chr1:169332546-169332973	GM12878	blood:	n/a	n/a
9	BATF	chr1:169332524-169332946	GM12878	blood:	n/a	chr1:169332732-169332743
10	EBF1	chr1:169332590-169332918	GM12878	blood:	n/a	n/a
11	MEF2A	chr1:169332492-169333042	GM12878	blood:	n/a	n/a
12	CREB1	chr1:169332509-169333006	GM12878	blood:	n/a	n/a
13	FOS	chr1:169332276-169333149	MCF10A-Er-Src	breast:	n/a	chr1:169332734-169332745
14	STAT5A	chr1:169332568-169332914	GM12878	blood:	n/a	n/a
15	FOS	chr1:169332292-169333184	MCF10A-Er-Src	breast:	n/a	chr1:169332734-169332745
16	TCF12	chr1:169332335-169333130	SK-N-SH	brain:	n/a	n/a
17	EBF1	chr1:169332642-169332912	GM12878	blood:	n/a	n/a
18	FOXM1	chr1:169332502-169333014	GM12878	blood:	n/a	n/a
19	RCOR1	chr1:169332646-169333012	GM12878	blood:	n/a	n/a
20	RUNX3	chr1:169332515-169333043	GM12878	blood:	n/a	n/a
21	MTA3	chr1:169332532-169333012	GM12878	blood:	n/a	n/a
22	JUND	chr1:169332245-169333079	SK-N-SH	brain:	n/a	chr1:169332734-169332745
23	FOS	chr1:169332430-169332921	Hela-S3	cervix:	n/a	chr1:169332734-169332745
24	POLR2A	chr1:169332666-169332901	Hela-S3	cervix:	n/a	n/a
25	STAT3	chr1:169332639-169332911	GM12878	blood:	n/a	n/a
26	FOSL2	chr1:169332274-169333048	SK-N-SH	brain:	n/a	n/a
27	JUN	chr1:169332500-169332929	Hela-S3	cervix:	n/a	n/a
28	FOS	chr1:169332275-169333010	MCF10A-Er-Src	breast:	n/a	chr1:169332734-169332745
29	JUND	chr1:169332535-169332978	HCT-116	colon:	n/a	chr1:169332734-169332745
30	STAT3	chr1:169332606-169333017	MCF10A-Er-Src	breast:	n/a	n/a
31	JUND	chr1:169332124-169333137	SK-N-SH	brain:	n/a	chr1:169332734-169332745
32	MYC	chr1:169332472-169332976	MCF10A-Er-Src	breast:	n/a	n/a
33	FOS	chr1:169332160-169332957	HUVEC	blood vessel:	n/a	chr1:169332734-169332745
34	FOS	chr1:169332276-169333222	MCF10A-Er-Src	breast:	n/a	chr1:169332734-169332745
35	IRF4	chr1:169332564-169332931	GM12878	blood:	n/a	n/a
36	BHLHE40	chr1:169332630-169332932	GM12878	blood:	n/a	n/a
37	JUND	chr1:169332316-169332982	HCT-116	colon:	n/a	chr1:169332734-169332745
38	POU2F2	chr1:169332641-169332961	GM12891	blood:	n/a	n/a
39	EP300	chr1:169332599-169332945	GM12878	blood:	n/a	n/a
40	EBF1	chr1:169332636-169332903	GM12878	blood:	n/a	n/a
41	NFIC	chr1:169332485-169333088	GM12878	blood:	n/a	n/a
42	JUN	chr1:169332275-169332912	HUVEC	blood vessel:	n/a	n/a
43	CREB1	chr1:169332532-169332952	GM12878	blood:	n/a	n/a
44	ATF2	chr1:169332499-169332994	GM12878	blood:	n/a	n/a
45	MYC	chr1:169332518-169332919	MCF10A-Er-Src	breast:	n/a	n/a
46	BCL11A	chr1:169332581-169332988	GM12878	blood:	n/a	n/a
47	POU2F2	chr1:169332616-169332901	GM12878	blood:	n/a	n/a
48	RUNX3	chr1:169332421-169333091	GM12878	blood:	n/a	n/a
49	FOSL1	chr1:169332486-169333000	HCT-116	colon:	n/a	n/a
50	CEBPB	chr1:169332568-169332932	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169331328..169334287-chr1:169334911..169337205,2	MCF-7	breast:
2	chr1:169075705..169078397-chr1:169329097..169333069,3	MCF-7	breast:
3	chr1:169332852..169334456-chr1:169336922..169338977,2	MCF-7	breast:

Variant related genes	Relation type
BLZF1	TF binding region
ENSG00000143153	Chromatin interaction
ENSG00000143156	Chromatin interaction
ENSG00000117475	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1014965	0.83[EUR][1000 genomes]
rs10442644	0.94[CEU][hapmap]
rs12116551	0.89[CEU][hapmap]
rs12118611	0.94[CEU][hapmap]
rs12119479	0.84[CEU][hapmap];0.83[AFR][1000 genomes]
rs12120007	0.89[CEU][hapmap]
rs12121891	0.87[CEU][hapmap];0.93[AFR][1000 genomes]
rs12121994	0.88[CEU][hapmap]
rs12124049	0.85[CEU][hapmap];0.83[AFR][1000 genomes]
rs12125501	0.94[CEU][hapmap]
rs12128350	0.81[CEU][hapmap]
rs12140572	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12143193	0.89[CEU][hapmap]
rs12143708	0.83[AFR][1000 genomes]
rs12145146	0.89[CEU][hapmap]
rs12145226	0.89[CEU][hapmap]
rs12728614	0.89[CEU][hapmap]
rs12730053	0.83[AFR][1000 genomes]
rs12733626	0.89[CEU][hapmap]
rs12750775	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12758228	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17349439	0.88[CEU][hapmap]
rs17349467	0.89[CEU][hapmap]
rs17577184	0.85[CEU][hapmap]
rs1936533	0.88[CEU][hapmap]
rs2040446	0.88[CEU][hapmap]
rs2157597	0.94[CEU][hapmap]
rs35010461	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs35107735	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs35220898	0.94[CEU][hapmap]
rs3766090	0.88[CEU][hapmap]
rs4589164	0.94[CEU][hapmap]
rs4656182	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4656658	0.88[CEU][hapmap]
rs4656664	0.88[CEU][hapmap]
rs4656671	0.84[CEU][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4656674	0.85[EUR][1000 genomes]
rs4656677	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4656678	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4656680	0.84[CEU][hapmap];0.88[AFR][1000 genomes]
rs61806989	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61807017	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6692649	0.80[CEU][hapmap]
rs7368145	0.93[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7522896	0.89[CEU][hapmap]
rs7527703	0.84[CEU][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7542751	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17349579	NME7	cis	Artery Tibial	GTEx
rs17349579	NME7	cis	Thyroid	GTEx
rs17349579	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs17349579	NME7	cis	Esophagus Muscularis	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:169305600-169336400	Weak transcription	Left Ventricle	heart
3	chr1:169309200-169333600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:169309400-169336400	Weak transcription	Ovary	ovary
5	chr1:169311000-169336400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:169316000-169334200	Weak transcription	Fetal Intestine Small	intestine
7	chr1:169317000-169336400	Weak transcription	Pancreas	Pancrea
8	chr1:169317200-169333800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:169317800-169333800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:169317800-169335800	Weak transcription	Fetal Lung	lung
11	chr1:169318200-169334000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:169324600-169335800	Weak transcription	Primary T cells from cord blood	blood
13	chr1:169325600-169335800	Weak transcription	K562	blood
14	chr1:169326200-169334200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:169327200-169335800	Weak transcription	Small Intestine	intestine
16	chr1:169327200-169336200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:169330000-169336400	Weak transcription	Psoas Muscle	Psoas
18	chr1:169330800-169335800	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:169330800-169336400	Weak transcription	Right Ventricle	heart
20	chr1:169331400-169335800	Weak transcription	Fetal Intestine Large	intestine
21	chr1:169331600-169333200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:169331600-169333400	Enhancers	Osteobl	bone
23	chr1:169331600-169335600	Enhancers	HMEC	breast
24	chr1:169331800-169333000	Enhancers	Placenta Amnion	Placenta Amnion
25	chr1:169331800-169333000	Enhancers	NHDF-Ad	bronchial
26	chr1:169331800-169333200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr1:169331800-169333400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:169331800-169333400	Enhancers	HUVEC	blood vessel
29	chr1:169331800-169333600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:169331800-169335800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:169331800-169336200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:169332000-169333600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr1:169332000-169334400	Enhancers	NHEK	skin
34	chr1:169332000-169335800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr1:169332200-169333200	Enhancers	Primary T cells fromperipheralblood	blood
36	chr1:169332200-169333200	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr1:169332200-169333200	Enhancers	HSMM	muscle
38	chr1:169332200-169333400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:169332200-169334200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:169332200-169336400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:169332400-169333200	Enhancers	NHLF	lung
42	chr1:169332600-169333000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:169332600-169333000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:169332600-169333000	Flanking Active TSS	GM12878-XiMat	blood
45	chr1:169332600-169333200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:169332600-169333200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:169332600-169333200	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr1:169332600-169333200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:169332600-169333200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:169332600-169333200	Enhancers	A549	lung

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