Variant report

Variant	rs17562676
Chromosome Location	chr19:45601581-45601582
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	chr19:45601442-45601912	K562	blood:	n/a	chr19:45601455-45601466 chr19:45601456-45601466 chr19:45601456-45601465 chr19:45601457-45601464
2	MYC	chr19:45601509-45601928	HepG2	liver:	n/a	n/a
3	JUN	chr19:45601523-45601901	K562	blood:	n/a	chr19:45601729-45601741 chr19:45601730-45601740 chr19:45601730-45601739 chr19:45601730-45601740 chr19:45601730-45601740 chr19:45601730-45601740
4	BHLHE40	chr19:45601400-45601883	HepG2	liver:	n/a	n/a
5	FOSL2	chr19:45601441-45602076	SK-N-SH	brain:	n/a	chr19:45601729-45601741 chr19:45601730-45601740 chr19:45601728-45601739 chr19:45601730-45601739 chr19:45601730-45601740 chr19:45601730-45601740 chr19:45601730-45601740
6	FOS	chr19:45601562-45601911	MCF10A-Er-Src	breast:	n/a	chr19:45601729-45601740 chr19:45601729-45601741 chr19:45601730-45601740 chr19:45601730-45601739 chr19:45601730-45601740 chr19:45601730-45601740 chr19:45601730-45601740
7	FOSL2	chr19:45601498-45602097	MCF-7	breast:	n/a	chr19:45601729-45601741 chr19:45601730-45601740 chr19:45601728-45601739 chr19:45601730-45601739 chr19:45601730-45601740 chr19:45601730-45601740 chr19:45601730-45601740
8	MAX	chr19:45601522-45601964	K562	blood:	n/a	n/a
9	MXI1	chr19:45600994-45601970	HepG2	liver:	n/a	chr19:45601457-45601466 chr19:45601455-45601464
10	HEY1	chr19:45600865-45601842	HepG2	liver:	n/a	chr19:45601456-45601465
11	POLR2A	chr19:45601146-45601887	MCF-7	breast:	n/a	n/a
12	EP300	chr19:45601526-45601963	HepG2	liver:	n/a	chr19:45601733-45601746
13	SIN3AK20	chr19:45601272-45602209	MCF-7	breast:	n/a	n/a
14	USF1	chr19:45601500-45601791	A549	lung:	n/a	n/a
15	NR2F2	chr19:45601337-45602068	K562	blood:	n/a	n/a
16	JUND	chr19:45601547-45601870	HepG2	liver:	n/a	chr19:45601729-45601741 chr19:45601730-45601740 chr19:45601730-45601739 chr19:45601730-45601740 chr19:45601730-45601740 chr19:45601730-45601740 chr19:45601729-45601740
17	MAX	chr19:45601564-45601837	NB4	blood:	n/a	n/a
18	MYC	chr19:45601439-45601887	K562	blood:	n/a	chr19:45601455-45601466 chr19:45601456-45601466 chr19:45601456-45601465 chr19:45601457-45601464
19	FOS	chr19:45601560-45601891	MCF10A-Er-Src	breast:	n/a	chr19:45601729-45601740 chr19:45601729-45601741 chr19:45601730-45601740 chr19:45601730-45601739 chr19:45601730-45601740 chr19:45601730-45601740 chr19:45601730-45601740
20	JUND	chr19:45601541-45601907	HepG2	liver:	n/a	chr19:45601729-45601741 chr19:45601730-45601740 chr19:45601730-45601739 chr19:45601730-45601740 chr19:45601730-45601740 chr19:45601730-45601740 chr19:45601729-45601740
21	USF2	chr19:45601311-45601836	HepG2	liver:	n/a	chr19:45601672-45601683 chr19:45601647-45601658
22	ATF1	chr19:45601561-45601855	K562	blood:	n/a	n/a
23	RCOR1	chr19:45601556-45601842	HepG2	liver:	n/a	n/a
24	TBL1XR1	chr19:45601479-45601682	K562	blood:	n/a	n/a
25	POLR2A	chr19:45601201-45601987	U87	brain:	n/a	n/a
26	FOSL1	chr19:45601562-45601928	K562	blood:	n/a	chr19:45601729-45601741 chr19:45601729-45601740 chr19:45601730-45601740 chr19:45601730-45601739 chr19:45601730-45601740 chr19:45601730-45601740 chr19:45601730-45601740
27	USF1	chr19:45601407-45601829	K562	blood:	n/a	n/a
28	JUN	chr19:45601402-45602151	K562	blood:	n/a	chr19:45601729-45601741 chr19:45601730-45601740 chr19:45601730-45601739 chr19:45601730-45601740 chr19:45601730-45601740 chr19:45601730-45601740
29	MAX	chr19:45601259-45601969	K562	blood:	n/a	chr19:45601455-45601466 chr19:45601456-45601466 chr19:45601456-45601465 chr19:45601457-45601464
30	USF1	chr19:45601422-45601962	K562	blood:	n/a	n/a
31	USF1	chr19:45601566-45601888	A549	lung:	n/a	n/a
32	USF1	chr19:45601531-45601760	HepG2	liver:	n/a	n/a
33	MAX	chr19:45600825-45602450	HepG2	liver:	n/a	chr19:45601455-45601466 chr19:45601456-45601466 chr19:45601456-45601465 chr19:45601457-45601464
34	MYC	chr19:45601551-45601863	MCF-7	breast:	n/a	n/a
35	USF1	chr19:45601506-45601829	SK-N-SH_RA	brain:	n/a	n/a
36	HEY1	chr19:45601415-45601795	HepG2	liver:	n/a	chr19:45601456-45601465
37	E2F6	chr19:45601515-45601801	K562	blood:	n/a	n/a
38	POLR2A	chr19:45601411-45601983	HepG2	liver:	n/a	n/a
39	FOSL2	chr19:45601470-45601920	A549	lung:	n/a	chr19:45601729-45601741 chr19:45601730-45601740 chr19:45601728-45601739 chr19:45601730-45601739 chr19:45601730-45601740 chr19:45601730-45601740 chr19:45601730-45601740
40	MYC	chr19:45601494-45601860	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr19:45601411-45602072	PFSK-1	brain:	n/a	n/a
42	KAP1	chr19:45601564-45601864	U2OS	brain:	n/a	chr19:45601729-45601738
43	MAX	chr19:45601238-45602052	A549	lung:	n/a	chr19:45601455-45601466 chr19:45601456-45601466 chr19:45601456-45601465 chr19:45601457-45601464
44	USF1	chr19:45601417-45601971	A549	lung:	n/a	n/a
45	MYC	chr19:45601559-45601879	MCF10A-Er-Src	breast:	n/a	n/a
46	MAX	chr19:45601262-45601989	SK-N-SH	brain:	n/a	chr19:45601455-45601466 chr19:45601456-45601466 chr19:45601456-45601465 chr19:45601457-45601464
47	POLR2A	chr19:45601501-45601941	SK-N-SH	brain:	n/a	n/a
48	USF1	chr19:45601518-45601845	HepG2	liver:	n/a	n/a
49	FOSL2	chr19:45601494-45601997	MCF-7	breast:	n/a	chr19:45601729-45601741 chr19:45601730-45601740 chr19:45601728-45601739 chr19:45601730-45601739 chr19:45601730-45601740 chr19:45601730-45601740 chr19:45601730-45601740
50	FOS	chr19:45601545-45601934	HUVEC	blood vessel:	n/a	chr19:45601729-45601740 chr19:45601729-45601741 chr19:45601730-45601740 chr19:45601730-45601739 chr19:45601730-45601740 chr19:45601730-45601740 chr19:45601730-45601740

No.	Distal block	Cell Line	Cell type
1	chr19:45572753..45574851-chr19:45600312..45603270,3	MCF-7	breast:
2	chr19:45600364..45603096-chr19:45634036..45635975,3	K562	blood:
3	chr19:45577259..45585589-chr19:45592358..45603656,27	K562	blood:
4	chr19:45599536..45601842-chr19:45680214..45683466,3	K562	blood:
5	chr19:45576493..45586900-chr19:45588536..45604492,49	MCF-7	breast:
6	chr19:45600305..45602430-chr19:45642699..45644377,2	K562	blood:
7	chr19:45578126..45585691-chr19:45599620..45604032,8	MCF-7	breast:
8	chr19:45600751..45603096-chr19:45634036..45635702,2	K562	blood:

Variant related genes	Relation type
PPP1R37	TF binding region
ENSG00000267545	Chromatin interaction
ENSG00000007255	Chromatin interaction
ENSG00000142252	Chromatin interaction
ENSG00000007047	Chromatin interaction
ENSG00000104859	Chromatin interaction
ENSG00000189114	Chromatin interaction
ENSG00000170684	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10403214	0.93[CEU][hapmap];0.98[EUR][1000 genomes]
rs10405306	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10405719	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10405721	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407374	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10408366	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10409138	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs10409232	0.91[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10409727	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10409903	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10410424	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10412988	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10417101	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417618	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417804	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10421932	0.92[CEU][hapmap]
rs10424651	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12459074	0.80[CEU][hapmap]
rs12459945	0.80[EUR][1000 genomes]
rs12461416	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1541926	1.00[EUR][1000 genomes]
rs17562787	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17642665	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1982077	1.00[EUR][1000 genomes]
rs2011438	0.80[EUR][1000 genomes]
rs4608431	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4803798	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248168	1.00[MKK][hapmap]
rs7253652	1.00[MKK][hapmap]
rs7257566	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7257599	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs733289	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73562250	0.80[EUR][1000 genomes]
rs73562267	0.80[EUR][1000 genomes]
rs8101046	0.80[EUR][1000 genomes]
rs8104024	1.00[MKK][hapmap]
rs8110379	1.00[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3449420	chr19:45523560-45626884	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17562676	DKKL1	cis	cerebellum	SCAN
rs17562676	NANOS2	cis	cerebellum	SCAN
rs17562676	EIF5AP3	cis	lung	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45597400-45601600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr19:45597400-45602200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr19:45597400-45602800	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr19:45597400-45603000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr19:45597400-45603000	Enhancers	Fetal Brain Male	brain
6	chr19:45597400-45603200	Enhancers	Left Ventricle	heart
7	chr19:45597400-45604600	Enhancers	Placenta	Placenta
8	chr19:45597400-45609400	Enhancers	Stomach Mucosa	stomach
9	chr19:45597600-45602000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr19:45597600-45603000	Enhancers	Primary T cells fromperipheralblood	blood
11	chr19:45597600-45603000	Enhancers	Lung	lung
12	chr19:45597600-45606200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:45597600-45609200	Enhancers	Pancreas	Pancrea
14	chr19:45597800-45602000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr19:45597800-45602600	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr19:45597800-45602800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr19:45597800-45603000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr19:45597800-45604000	Genic enhancers	Fetal Muscle Leg	muscle
19	chr19:45597800-45604200	Enhancers	Psoas Muscle	Psoas
20	chr19:45598000-45604000	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr19:45598200-45601800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr19:45598200-45604400	Enhancers	Gastric	stomach
23	chr19:45598200-45606000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr19:45598400-45601600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr19:45598400-45602200	Enhancers	Colon Smooth Muscle	Colon
26	chr19:45598400-45602400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr19:45598400-45604000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr19:45598400-45605600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:45598400-45606000	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr19:45598400-45606000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr19:45598400-45606000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr19:45598400-45606600	Genic enhancers	Fetal Intestine Small	intestine
33	chr19:45598600-45602800	Enhancers	Liver	Liver
34	chr19:45599000-45601600	Enhancers	Brain Substantia Nigra	brain
35	chr19:45599000-45602600	Enhancers	Ovary	ovary
36	chr19:45599000-45603600	Genic enhancers	Fetal Thymus	thymus
37	chr19:45599200-45603600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr19:45599200-45603600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr19:45599400-45601600	Genic enhancers	Fetal Brain Female	brain
40	chr19:45599400-45601800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr19:45599400-45605800	Weak transcription	Primary B cells from peripheral blood	blood
42	chr19:45599600-45601800	Genic enhancers	Dnd41	blood
43	chr19:45599800-45602200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr19:45599800-45603000	Genic enhancers	Spleen	Spleen
45	chr19:45599800-45605800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr19:45600000-45603800	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr19:45600000-45604000	Enhancers	HMEC	breast
48	chr19:45600000-45604400	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr19:45600000-45606200	Enhancers	Fetal Intestine Large	intestine
50	chr19:45600000-45607800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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