Variant report

Variant	rs1809054
Chromosome Location	chr16:77619774-77619775
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	FOS	chr16:77619756-77620251	MCF10A-Er-Src	breast:	n/a	chr16:77619931-77619939 chr16:77619960-77619968 chr16:77619929-77619941 chr16:77619930-77619940 chr16:77620159-77620173 chr16:77619959-77619969 chr16:77619930-77619940 chr16:77620014-77620023
2	NFIC	chr16:77619734-77620164	ECC-1	luminal epithelium:	n/a	chr16:77619854-77619870 chr16:77619853-77619870
3	POLR2A	chr16:77618532-77620235	U87	brain:	n/a	n/a
4	MAX	chr16:77619752-77620171	ECC-1	luminal epithelium:	n/a	chr16:77619856-77619867 chr16:77619960-77619969 chr16:77619857-77619866 chr16:77619931-77619940 chr16:77619857-77619864
5	JUN	chr16:77619010-77620236	HUVEC	blood vessel:	n/a	chr16:77619931-77619939 chr16:77619960-77619968 chr16:77619434-77619446 chr16:77619929-77619941 chr16:77619930-77619940 chr16:77619421-77619430 chr16:77620159-77620173 chr16:77619959-77619969 chr16:77619930-77619940 chr16:77620014-77620023
6	POLR2A	chr16:77619051-77620297	HUVEC	blood vessel:	n/a	n/a
7	FOSL2	chr16:77619651-77620202	SK-N-SH	brain:	n/a	chr16:77619931-77619939 chr16:77619960-77619968 chr16:77619929-77619941 chr16:77619930-77619940 chr16:77620159-77620173 chr16:77619959-77619969 chr16:77619930-77619940 chr16:77620014-77620023
8	TCF12	chr16:77619656-77620277	SK-N-SH	brain:	n/a	n/a
9	NFIC	chr16:77619652-77620241	SK-N-SH	brain:	n/a	chr16:77619854-77619870 chr16:77619853-77619870
10	POLR2A	chr16:77618140-77622223	HUVEC	blood vessel:	n/a	n/a
11	MAX	chr16:77619654-77620153	A549	lung:	n/a	chr16:77619856-77619867 chr16:77619960-77619969 chr16:77619857-77619866 chr16:77619931-77619940 chr16:77619857-77619864
12	POLR2A	chr16:77618395-77620324	U87	brain:	n/a	n/a
13	FOS	chr16:77619196-77620291	MCF10A-Er-Src	breast:	n/a	chr16:77619931-77619939 chr16:77619960-77619968 chr16:77619434-77619446 chr16:77619929-77619941 chr16:77619930-77619940 chr16:77619421-77619430 chr16:77620159-77620173 chr16:77619959-77619969 chr16:77619930-77619940 chr16:77620014-77620023
14	TCF12	chr16:77619746-77620298	ECC-1	luminal epithelium:	n/a	n/a
15	JUND	chr16:77619618-77620215	HCT-116	colon:	n/a	chr16:77619931-77619939 chr16:77619960-77619968 chr16:77619929-77619941 chr16:77619930-77619940 chr16:77620159-77620173 chr16:77619959-77619969 chr16:77619930-77619940 chr16:77620014-77620023
16	FOSL1	chr16:77619764-77620205	HCT-116	colon:	n/a	chr16:77619931-77619939 chr16:77619960-77619968 chr16:77619929-77619941 chr16:77619930-77619940 chr16:77620159-77620173 chr16:77619959-77619969 chr16:77619930-77619940 chr16:77620014-77620023
17	STAT3	chr16:77619273-77620271	MCF10A-Er-Src	breast:	n/a	n/a
18	FOSL2	chr16:77619645-77620274	A549	lung:	n/a	chr16:77619931-77619939 chr16:77619960-77619968 chr16:77619929-77619941 chr16:77619930-77619940 chr16:77620159-77620173 chr16:77619959-77619969 chr16:77619930-77619940 chr16:77620014-77620023
19	STAT3	chr16:77619687-77620273	MCF10A-Er-Src	breast:	n/a	n/a
20	GATA3	chr16:77619728-77620154	SK-N-SH	brain:	n/a	chr16:77619929-77619936
21	POLR2A	chr16:77618255-77620411	HUVEC	blood vessel:	n/a	n/a
22	MYC	chr16:77619694-77620249	MCF10A-Er-Src	breast:	n/a	chr16:77619856-77619867 chr16:77619960-77619969 chr16:77619857-77619866 chr16:77619931-77619940 chr16:77619857-77619864
23	FOS	chr16:77619196-77620283	MCF10A-Er-Src	breast:	n/a	chr16:77619931-77619939 chr16:77619960-77619968 chr16:77619434-77619446 chr16:77619929-77619941 chr16:77619930-77619940 chr16:77619421-77619430 chr16:77620159-77620173 chr16:77619959-77619969 chr16:77619930-77619940 chr16:77620014-77620023
24	FOSL2	chr16:77619761-77620097	A549	lung:	n/a	chr16:77619931-77619939 chr16:77619960-77619968 chr16:77619929-77619941 chr16:77619930-77619940 chr16:77619959-77619969 chr16:77619930-77619940 chr16:77620014-77620023
25	BACH1	chr16:77619774-77620152	H1-hESC	embryonic stem cell:	n/a	chr16:77619957-77619971
26	TCF12	chr16:77619658-77620282	ECC-1	luminal epithelium:	n/a	n/a
27	GATA3	chr16:77619650-77620286	SK-N-SH	brain:	n/a	chr16:77619929-77619936 chr16:77619709-77619719
28	TCF12	chr16:77619633-77620261	A549	lung:	n/a	n/a
29	MAX	chr16:77619654-77620269	A549	lung:	n/a	chr16:77619856-77619867 chr16:77619960-77619969 chr16:77619857-77619866 chr16:77619931-77619940 chr16:77619857-77619864
30	FOS	chr16:77619127-77620324	HUVEC	blood vessel:	n/a	chr16:77619931-77619939 chr16:77619960-77619968 chr16:77619434-77619446 chr16:77619929-77619941 chr16:77619930-77619940 chr16:77619421-77619430 chr16:77620159-77620173 chr16:77619959-77619969 chr16:77619930-77619940 chr16:77620014-77620023
31	GATA2	chr16:77618759-77620372	HUVEC	blood vessel:	n/a	chr16:77619929-77619936 chr16:77619709-77619719
32	MAX	chr16:77619621-77620264	HCT-116	colon:	n/a	chr16:77619856-77619867 chr16:77619960-77619969 chr16:77619857-77619866 chr16:77619931-77619940 chr16:77619857-77619864
33	MYC	chr16:77619236-77620191	MCF10A-Er-Src	breast:	n/a	chr16:77619856-77619867 chr16:77619960-77619969 chr16:77619857-77619866 chr16:77619931-77619940 chr16:77619857-77619864
34	STAT3	chr16:77619154-77620346	MCF10A-Er-Src	breast:	n/a	n/a
35	NFIC	chr16:77619617-77620317	ECC-1	luminal epithelium:	n/a	chr16:77619854-77619870 chr16:77619853-77619870
36	STAT3	chr16:77619273-77620272	MCF10A-Er-Src	breast:	n/a	n/a
37	GATA3	chr16:77619634-77620243	A549	lung:	n/a	chr16:77619929-77619936 chr16:77619709-77619719
38	JUND	chr16:77619653-77620241	HCT-116	colon:	n/a	chr16:77619931-77619939 chr16:77619960-77619968 chr16:77619929-77619941 chr16:77619930-77619940 chr16:77620159-77620173 chr16:77619959-77619969 chr16:77619930-77619940 chr16:77620014-77620023
39	EP300	chr16:77619653-77620321	ECC-1	luminal epithelium:	n/a	n/a
40	FOSL1	chr16:77619629-77620321	HCT-116	colon:	n/a	chr16:77619931-77619939 chr16:77619960-77619968 chr16:77619929-77619941 chr16:77619930-77619940 chr16:77620159-77620173 chr16:77619959-77619969 chr16:77619930-77619940 chr16:77620014-77620023
41	FOS	chr16:77619149-77620336	MCF10A-Er-Src	breast:	n/a	chr16:77619931-77619939 chr16:77619960-77619968 chr16:77619434-77619446 chr16:77619929-77619941 chr16:77619930-77619940 chr16:77619421-77619430 chr16:77620159-77620173 chr16:77619959-77619969 chr16:77619930-77619940 chr16:77620014-77620023
42	POLR2A	chr16:77619041-77620146	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr16:77619172-77619831	HUVEC	blood vessel:	n/a	n/a
44	SP1	chr16:77619706-77620257	A549	lung:	n/a	n/a
45	POLR2A	chr16:77618589-77620300	U87	brain:	n/a	n/a
46	PBX3	chr16:77619696-77620200	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:77619466..77621855-chr16:77621914..77626371,4	MCF-7	breast:
2	chr16:77617063..77620231-chr16:77635961..77639482,4	MCF-7	breast:
3	chr16:77619730..77621519-chr16:77627821..77630581,2	MCF-7	breast:
4	chr16:77269962..77270537-chr16:77619167..77620058,2	MCF-7	breast:
5	chr16:77618149..77620811-chr16:77638039..77640626,2	MCF-7	breast:
6	chr16:77619040..77621294-chr16:77626377..77629005,2	MCF-7	breast:
7	chr16:77618368..77620113-chr16:77693748..77695802,3	MCF-7	breast:
8	chr16:77619452..77621182-chr16:77622487..77625423,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261154	TF binding region
ENSG00000261154	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12444341	1.00[JPT][hapmap]
rs1809055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280881	1.00[JPT][hapmap]
rs280882	1.00[CHB][hapmap];0.83[GIH][hapmap]
rs371896	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs376156	1.00[JPT][hapmap]
rs392001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs393951	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs400226	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs416187	1.00[JPT][hapmap]
rs428800	1.00[CHB][hapmap]
rs437991	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs452742	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs615153	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065048	chr16:77003426-77675163	Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	esv2830376	chr16:77014551-77658185	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv1065149	chr16:77032082-77671890	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1056676	chr16:77139682-77854848	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv1059194	chr16:77281068-77745928	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv542969	chr16:77281068-77745928	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1061875	chr16:77451850-78003403	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv906957	chr16:77457066-77643421	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv869119	chr16:77458671-78008053	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv521833	chr16:77516263-77819441	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv906958	chr16:77535643-77684529	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv532564	chr16:77549380-78143752	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
13	nsv1057595	chr16:77574148-77898842	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv833291	chr16:77593616-77627962	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv906959	chr16:77608310-77657120	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv1060068	chr16:77615499-78353775	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1809054	CD3D	trans	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:77609400-77626600	Weak transcription	Right Atrium	heart
2	chr16:77616600-77619800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr16:77616600-77624400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr16:77617200-77621800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr16:77617400-77620600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr16:77618000-77620600	Enhancers	A549	lung
7	chr16:77618200-77621400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr16:77618800-77620000	Weak transcription	Adipose Nuclei	Adipose
9	chr16:77619200-77620200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr16:77619200-77620200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr16:77619400-77619800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr16:77619400-77619800	Flanking Active TSS	NH-A	brain
13	chr16:77619400-77620000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr16:77619400-77620000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr16:77619400-77620200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr16:77619400-77620200	Enhancers	NHEK	skin
17	chr16:77619400-77620800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr16:77619400-77621000	Enhancers	HMEC	breast
19	chr16:77619400-77622000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr16:77619600-77619800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr16:77619600-77619800	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr16:77619600-77619800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr16:77619600-77620000	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr16:77619600-77620000	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr16:77619600-77620000	Flanking Active TSS	HUVEC	blood vessel
26	chr16:77619600-77620200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr16:77619600-77620200	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr16:77619600-77620200	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr16:77619600-77620800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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