Variant report

Variant	rs17079679
Chromosome Location	chr5:179266475-179266476
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:98)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:98 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr5:179266218-179266518	A549	lung:	n/a	n/a
2	POLR2A	chr5:179266083-179267145	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr5:179262507-179269414	PANC-1	pancreas:	n/a	n/a
4	MTA3	chr5:179266158-179266852	GM12878	blood:	n/a	n/a
5	POLR2A	chr5:179262587-179266982	Hela-S3	cervix:	n/a	n/a
6	REST	chr5:179266184-179266953	A549	lung:	n/a	chr5:179266660-179266673
7	POLR2A	chr5:179266135-179269441	U87	brain:	n/a	n/a
8	POLR2A	chr5:179266065-179267056	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:179262501-179268119	K562	blood:	n/a	n/a
10	POLR2A	chr5:179266250-179266866	HepG2	liver:	n/a	n/a
11	SIN3AK20	chr5:179266198-179266956	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr5:179266463-179266959	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr5:179266187-179266942	HepG2	liver:	n/a	n/a
14	POLR2A	chr5:179266164-179266780	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr5:179266181-179266877	HepG2	liver:	n/a	n/a
16	POLR2A	chr5:179266191-179267047	MCF-7	breast:	n/a	n/a
17	POLR2A	chr5:179266227-179266897	HepG2	liver:	n/a	n/a
18	JUND	chr5:179264368-179267131	A549	lung:	n/a	n/a
19	POLR2A	chr5:179266251-179266507	GM12878	blood:	n/a	n/a
20	POLR2A	chr5:179266286-179266808	GM12878	blood:	n/a	n/a
21	POLR2A	chr5:179263086-179269260	IMR90	lung:	n/a	n/a
22	POLR2A	chr5:179266236-179266910	HepG2	liver:	n/a	n/a
23	JUND	chr5:179266172-179267035	A549	lung:	n/a	n/a
24	POLR2A	chr5:179263016-179266976	HepG2	liver:	n/a	n/a
25	ZBTB33	chr5:179266375-179266825	A549	lung:	n/a	n/a
26	TCF12	chr5:179266214-179266890	A549	lung:	n/a	chr5:179266813-179266823
27	POLR2A	chr5:179263338-179269338	MCF10A-Er-Src	breast:	n/a	n/a
28	JUND	chr5:179266238-179266481	HepG2	liver:	n/a	n/a
29	POLR2A	chr5:179262885-179267061	PFSK-1	brain:	n/a	n/a
30	TCF12	chr5:179265633-179267064	A549	lung:	n/a	chr5:179266813-179266823
31	PBX3	chr5:179266138-179267072	A549	lung:	n/a	n/a
32	POLR2A	chr5:179266219-179266976	GM12892	blood:	n/a	n/a
33	POLR2A	chr5:179266265-179267086	A549	lung:	n/a	n/a
34	POLR2A	chr5:179262516-179269530	A549	lung:	n/a	n/a
35	CHD2	chr5:179266339-179266746	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr5:179266187-179266806	GM12891	blood:	n/a	n/a
37	POLR2A	chr5:179263068-179266984	Hela-S3	cervix:	n/a	n/a
38	ELF1	chr5:179266245-179267012	A549	lung:	n/a	n/a
39	REST	chr5:179266221-179266734	A549	lung:	n/a	chr5:179266660-179266673
40	POLR2A	chr5:179266070-179266998	GM12892	blood:	n/a	n/a
41	POLR2A	chr5:179266145-179266904	GM12892	blood:	n/a	n/a
42	POLR2A	chr5:179266156-179266948	A549	lung:	n/a	n/a
43	USF1	chr5:179266266-179266964	A549	lung:	n/a	n/a
44	POLR2A	chr5:179266049-179269325	U87	brain:	n/a	n/a
45	PBX3	chr5:179266162-179266991	A549	lung:	n/a	n/a
46	GATA3	chr5:179266175-179267134	A549	lung:	n/a	n/a
47	SMC3	chr5:179266449-179266502	HepG2	liver:	n/a	n/a
48	POLR2A	chr5:179266266-179266861	GM12878	blood:	n/a	n/a
49	POLR2A	chr5:179263029-179266942	K562	blood:	n/a	n/a
50	POLR2A	chr5:179266119-179266924	Hela-S3	cervix:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179204097..179205986-chr5:179266401..179268653,2	K562	blood:
2	chr5:179265203..179267411-chr5:179270940..179272885,3	MCF-7	breast:

No data

Variant related genes	Relation type
C5orf45	TF binding region
ENSG00000161010	Chromatin interaction
ENSG00000222448	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10040357	1.00[EUR][1000 genomes]
rs10058037	1.00[EUR][1000 genomes]
rs10069530	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10078686	1.00[MEX][hapmap]
rs11743197	1.00[EUR][1000 genomes]
rs13356823	1.00[EUR][1000 genomes]
rs13358321	1.00[EUR][1000 genomes]
rs156099	1.00[EUR][1000 genomes]
rs1960428	1.00[EUR][1000 genomes]
rs269459	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs269460	1.00[EUR][1000 genomes]
rs272440	1.00[MEX][hapmap]
rs28656195	1.00[EUR][1000 genomes]
rs56844432	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57000847	1.00[EUR][1000 genomes]
rs57104438	1.00[EUR][1000 genomes]
rs57141821	1.00[EUR][1000 genomes]
rs57356486	1.00[EUR][1000 genomes]
rs58007232	1.00[EUR][1000 genomes]
rs58225020	1.00[EUR][1000 genomes]
rs58586529	1.00[EUR][1000 genomes]
rs58899481	1.00[EUR][1000 genomes]
rs60407359	1.00[EUR][1000 genomes]
rs60822577	1.00[EUR][1000 genomes]
rs61330504	1.00[EUR][1000 genomes]
rs6863030	1.00[EUR][1000 genomes]
rs6872508	1.00[EUR][1000 genomes]
rs73810492	1.00[EUR][1000 genomes]
rs73810493	1.00[EUR][1000 genomes]
rs73810929	1.00[EUR][1000 genomes]
rs7717213	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv883275	chr5:179193598-179267783	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
7	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
8	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
9	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
10	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers 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 miRNA target site	189 gene(s)	inside rSNPs	diseases
11	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers 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 miRNA target site	175 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179250200-179272000	Strong transcription	Fetal Muscle Leg	muscle
2	chr5:179250200-179272800	Weak transcription	Fetal Brain Male	brain
3	chr5:179251800-179267800	Strong transcription	Fetal Muscle Trunk	muscle
4	chr5:179255000-179268800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:179255200-179269000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:179258200-179274800	Weak transcription	Fetal Heart	heart
7	chr5:179262400-179266600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:179262400-179267000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr5:179262400-179267400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:179262400-179268600	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr5:179262400-179269000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:179262400-179269200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:179262400-179269400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:179262400-179269400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:179262400-179269400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:179262400-179269400	Strong transcription	Brain Angular Gyrus	brain
17	chr5:179262400-179271000	Strong transcription	Fetal Stomach	stomach
18	chr5:179262400-179271400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:179262400-179271600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:179262400-179272000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr5:179262600-179269000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:179262600-179269000	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr5:179262600-179269200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr5:179262600-179279400	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr5:179262800-179266800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr5:179262800-179269200	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr5:179263000-179267000	Genic enhancers	A549	lung
28	chr5:179263000-179268200	Strong transcription	Primary B cells from cord blood	blood
29	chr5:179263000-179269000	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr5:179263000-179269200	Strong transcription	Primary T cells from cord blood	blood
31	chr5:179263000-179269800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:179263000-179271000	Strong transcription	Brain Germinal Matrix	brain
33	chr5:179263000-179271400	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:179263000-179271800	Strong transcription	Fetal Lung	lung
35	chr5:179263000-179279600	Strong transcription	Brain Anterior Caudate	brain
36	chr5:179263000-179279800	Strong transcription	Brain Hippocampus Middle	brain
37	chr5:179263000-179280400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr5:179263200-179267200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr5:179263200-179268200	Strong transcription	Thymus	Thymus
40	chr5:179263200-179269000	Strong transcription	Brain Substantia Nigra	brain
41	chr5:179263200-179269600	Strong transcription	Fetal Brain Female	brain
42	chr5:179263600-179266600	Weak transcription	Right Atrium	heart
43	chr5:179263600-179267800	Strong transcription	Adipose Nuclei	Adipose
44	chr5:179263600-179280200	Strong transcription	Colon Smooth Muscle	Colon
45	chr5:179263800-179268200	Strong transcription	NHLF	lung
46	chr5:179263800-179269000	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr5:179263800-179269000	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr5:179263800-179269000	Strong transcription	Rectal Smooth Muscle	rectum
49	chr5:179263800-179269200	Strong transcription	Placenta	Placenta
50	chr5:179263800-179271000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links