Variant report

Variant	rs4792619
Chromosome Location	chr17:15406661-15406662
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:15406129-15406753	K562	blood:	n/a	n/a
2	CTCF	chr17:15406613-15406662	GM19240	blood:	n/a	n/a
3	CTCF	chr17:15406089-15406720	GM12878	blood:	n/a	n/a
4	SMC3	chr17:15405812-15406689	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr17:15406577-15406685	GM12892	blood:	n/a	n/a
6	MAX	chr17:15406071-15406730	A549	lung:	n/a	n/a
7	POLR2A	chr17:15405279-15408288	K562	blood:	n/a	n/a
8	CTCF	chr17:15406560-15406710	AG04449	skin:	n/a	n/a
9	CTCF	chr17:15406600-15406750	HEEpiC	esophagus:	n/a	n/a
10	E2F6	chr17:15406140-15406781	H1-hESC	embryonic stem cell:	n/a	n/a
11	PAX5	chr17:15406516-15406839	GM12878	blood:	n/a	n/a
12	PAX5	chr17:15406372-15406892	GM12878	blood:	n/a	n/a
13	ZNF143	chr17:15406106-15406720	GM12878	blood:	n/a	n/a
14	TCF12	chr17:15405873-15406682	A549	lung:	n/a	n/a
15	CTCF	chr17:15406600-15406680	GM19238	blood:	n/a	n/a
16	CTCF	chr17:15406604-15406718	GM19239	blood:	n/a	n/a
17	MAZ	chr17:15405514-15406698	IMR90	lung:	n/a	n/a
18	CTCF	chr17:15406640-15406790	AG09319	gingival:	n/a	n/a
19	PAX5	chr17:15406564-15406815	GM12878	blood:	n/a	n/a
20	CTCF	chr17:15405519-15407085	A549	lung:	n/a	n/a
21	CTCF	chr17:15406601-15406703	GM10266	blood:	n/a	n/a
22	CTCF	chr17:15406620-15406770	GM12866	blood:	n/a	n/a
23	CTCF	chr17:15405580-15406963	SK-N-SH	brain:	n/a	n/a
24	CTCF	chr17:15406595-15406677	GM12891	blood:	n/a	n/a
25	RAD21	chr17:15405727-15407299	SK-N-SH	brain:	n/a	n/a
26	CTCF	chr17:15406620-15406770	WI-38	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:15164289..15164844-chr17:15406132..15406721,2	K562	blood:
2	chr17:15160379..15161319-chr17:15405087..15406751,8	MCF-7	breast:
3	chr17:15165016..15165581-chr17:15405777..15406684,2	MCF-7	breast:
4	chr17:15163915..15164727-chr17:15406027..15406796,2	MCF-7	breast:
5	chr17:15339768..15340717-chr17:15405925..15406718,2	K562	blood:
6	chr17:15162964..15164800-chr17:15405391..15407046,14	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000223878	TF binding region
ENSG00000109099	Chromatin interaction
ENSG00000265445	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10153259	0.83[ASN][1000 genomes]
rs12450262	0.87[ASN][1000 genomes]
rs12450302	0.87[ASN][1000 genomes]
rs12450921	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12451284	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12452965	0.83[ASN][1000 genomes]
rs12453059	0.81[ASN][1000 genomes]
rs12453117	0.83[ASN][1000 genomes]
rs12938444	0.87[ASN][1000 genomes]
rs12943480	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12948266	0.87[ASN][1000 genomes]
rs12953212	0.87[ASN][1000 genomes]
rs17702522	0.87[ASN][1000 genomes]
rs17702771	0.81[ASN][1000 genomes]
rs2013835	0.87[ASN][1000 genomes]
rs2532479	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2654261	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34236889	0.87[ASN][1000 genomes]
rs34358805	0.83[ASN][1000 genomes]
rs34453320	0.87[ASN][1000 genomes]
rs34818581	0.83[ASN][1000 genomes]
rs35078459	0.87[ASN][1000 genomes]
rs35406616	0.87[ASN][1000 genomes]
rs35448233	0.87[ASN][1000 genomes]
rs35699886	0.87[ASN][1000 genomes]
rs36097878	0.83[ASN][1000 genomes]
rs3852809	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3911955	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4054418	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4791625	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6502459	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6502462	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71367505	0.85[ASN][1000 genomes]
rs71367507	0.81[ASN][1000 genomes]
rs716388	0.87[ASN][1000 genomes]
rs7226342	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7359507	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7359511	0.81[ASN][1000 genomes]
rs8064461	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8068610	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8070714	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8071082	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8074456	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs917567	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv949172	chr17:15206970-15416808	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1055677	chr17:15294011-15561130	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv1058286	chr17:15315763-15561130	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv543213	chr17:15315763-15561130	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4792619	AC005517.3	cis	Thyroid	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15383200-15419600	Weak transcription	Thymus	Thymus
2	chr17:15383400-15455000	Weak transcription	Gastric	stomach
3	chr17:15385600-15418000	Weak transcription	Pancreas	Pancrea
4	chr17:15387200-15417000	Weak transcription	Small Intestine	intestine
5	chr17:15393400-15451200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr17:15394600-15417000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr17:15394800-15450800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr17:15395000-15410200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr17:15395400-15413400	Weak transcription	Hela-S3	cervix
10	chr17:15396000-15417200	Weak transcription	Fetal Brain Male	brain
11	chr17:15396800-15420400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr17:15398800-15408800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr17:15399000-15408800	Strong transcription	HepG2	liver
14	chr17:15400800-15413000	Weak transcription	NH-A	brain
15	chr17:15401200-15420400	Weak transcription	Psoas Muscle	Psoas
16	chr17:15402800-15410200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr17:15403000-15410200	Weak transcription	Fetal Brain Female	brain
18	chr17:15404600-15406800	Enhancers	Fetal Kidney	kidney
19	chr17:15404600-15406800	Enhancers	HUVEC	blood vessel
20	chr17:15405000-15406800	Enhancers	Esophagus	oesophagus
21	chr17:15405000-15406800	Enhancers	Spleen	Spleen
22	chr17:15405200-15406800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr17:15405400-15406800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr17:15405400-15410200	Weak transcription	Primary T cells from cord blood	blood
25	chr17:15405400-15418200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr17:15405400-15419000	Weak transcription	Liver	Liver
27	chr17:15405600-15410200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr17:15405600-15411200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr17:15405800-15406800	Enhancers	H9 Cell Line	embryonic stem cell
30	chr17:15405800-15406800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr17:15405800-15406800	Enhancers	Primary B cells from peripheral blood	blood
32	chr17:15405800-15406800	Enhancers	Primary T cells fromperipheralblood	blood
33	chr17:15405800-15406800	Enhancers	Placenta	Placenta
34	chr17:15405800-15406800	Enhancers	HMEC	breast
35	chr17:15406000-15406800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr17:15406000-15406800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr17:15406000-15406800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr17:15406000-15406800	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr17:15406000-15406800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr17:15406000-15406800	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr17:15406000-15406800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr17:15406000-15406800	Enhancers	A549	lung
43	chr17:15406000-15406800	Enhancers	GM12878-XiMat	blood
44	chr17:15406000-15407000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr17:15406000-15407800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr17:15406000-15410200	Weak transcription	Fetal Intestine Large	intestine
47	chr17:15406000-15411600	Weak transcription	Lung	lung
48	chr17:15406000-15411800	Weak transcription	HSMMtube	muscle
49	chr17:15406000-15416800	Weak transcription	K562	blood
50	chr17:15406200-15406800	Enhancers	H1 Cell Line	embryonic stem cell

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