Variant report

Variant	rs4975679
Chromosome Location	chr5:1635899-1635900
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	IRF4	chr5:1635466-1636132	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:1635466-1636230	GM12878	blood:	n/a	n/a
3	PBX3	chr5:1635737-1636038	GM12878	blood:	n/a	n/a
4	POLR2A	chr5:1635686-1636373	GM12878	blood:	n/a	n/a
5	BATF	chr5:1635467-1636215	GM12878	blood:	n/a	n/a
6	EP300	chr5:1635612-1636127	GM12878	blood:	n/a	chr5:1636057-1636066 chr5:1635788-1635797
7	POU2F2	chr5:1635494-1636636	GM12891	blood:	n/a	chr5:1635811-1635824
8	BATF	chr5:1635405-1636089	GM12878	blood:	n/a	n/a
9	IRF4	chr5:1635306-1636340	GM12878	blood:	n/a	n/a
10	ZBTB33	chr5:1635656-1636067	GM12878	blood:	n/a	n/a
11	TCF3	chr5:1635650-1636054	GM12878	blood:	n/a	n/a
12	SP1	chr5:1635470-1636191	GM12878	blood:	n/a	n/a
13	RXRA	chr5:1635640-1636084	GM12878	blood:	n/a	chr5:1635788-1635797
14	NFIC	chr5:1635449-1635950	GM12878	blood:	n/a	n/a
15	POU2F2	chr5:1635046-1636581	GM12891	blood:	n/a	chr5:1635811-1635824 chr5:1635456-1635469 chr5:1635454-1635468 chr5:1635456-1635469 chr5:1635457-1635471
16	RUNX3	chr5:1635672-1635916	GM12878	blood:	n/a	n/a
17	POLR2A	chr5:1635464-1636183	GM12891	blood:	n/a	n/a
18	EP300	chr5:1635735-1636019	GM12878	blood:	n/a	chr5:1635788-1635797
19	FOSL2	chr5:1635749-1636010	HepG2	liver:	n/a	chr5:1635787-1635797 chr5:1635788-1635795 chr5:1635788-1635796
20	EBF1	chr5:1635466-1636129	GM12878	blood:	n/a	n/a
21	PAX5	chr5:1635503-1636158	GM12878	blood:	n/a	n/a
22	BCL11A	chr5:1635428-1636092	GM12878	blood:	n/a	chr5:1635788-1635797 chr5:1635787-1635796
23	NFIC	chr5:1635444-1636026	GM12878	blood:	n/a	n/a
24	TCF12	chr5:1635708-1636003	GM12878	blood:	n/a	n/a
25	PAX5	chr5:1635675-1635978	GM12878	blood:	n/a	n/a
26	TCF12	chr5:1635660-1635982	GM12878	blood:	n/a	n/a
27	GATA2	chr5:1635808-1636081	K562	blood:	n/a	n/a
28	PBX3	chr5:1635771-1635994	GM12878	blood:	n/a	n/a
29	BCL11A	chr5:1635660-1636035	GM12878	blood:	n/a	chr5:1635788-1635797 chr5:1635787-1635796
30	PAX5	chr5:1635735-1636013	GM12878	blood:	n/a	n/a
31	EBF1	chr5:1635558-1636072	GM12878	blood:	n/a	n/a
32	POU2F2	chr5:1635355-1636427	GM12878	blood:	n/a	chr5:1635811-1635824 chr5:1635456-1635469 chr5:1635454-1635468 chr5:1635456-1635469 chr5:1635457-1635471
33	POU2F2	chr5:1635664-1635981	GM12878	blood:	n/a	chr5:1635811-1635824
34	SP1	chr5:1635467-1636075	GM12878	blood:	n/a	n/a
35	PAX5	chr5:1635720-1636014	GM12878	blood:	n/a	n/a
36	RUNX3	chr5:1635556-1635932	GM12878	blood:	n/a	n/a
37	FOXM1	chr5:1635504-1635961	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:52596128..52598397-chr5:1635134..1637588,2	MCF-7	breast:
2	chr5:1524111..1525678-chr5:1634635..1636646,2	K562	blood:

Variant related genes	Relation type
ENSG00000188002	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11747600	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12658097	0.95[ASN][1000 genomes]
rs12658927	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13158448	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13181671	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1968011	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2354149	0.88[ASN][1000 genomes]
rs34192949	0.85[ASN][1000 genomes]
rs4975672	0.93[ASN][1000 genomes]
rs4975674	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4975675	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4975678	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975681	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6881649	0.87[ASN][1000 genomes]
rs7700984	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv880740	chr5:1468287-1671200	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS 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	49 gene(s)	inside rSNPs	diseases
3	nsv881554	chr5:1468287-1696932	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
4	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
5	nsv881096	chr5:1503610-1671200	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
6	nsv964815	chr5:1608931-1639317	Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv880390	chr5:1612612-1653418	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv880788	chr5:1629407-1671200	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	esv19841	chr5:1631508-1636570	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4975679	LOC728613	Cis_1M	lymphoblastoid	RTeQTL
rs4975679	LOC728613///PDCD6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1634600-1636400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr5:1634600-1645000	Weak transcription	Right Atrium	heart
3	chr5:1634600-1645200	Weak transcription	Gastric	stomach
4	chr5:1634800-1636600	Enhancers	Muscle Satellite Cultured Cells	--
5	chr5:1635000-1636600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:1635200-1636600	Enhancers	Fetal Stomach	stomach
7	chr5:1635200-1637200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:1635200-1640000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:1635400-1636400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:1635400-1636400	Enhancers	GM12878-XiMat	blood
11	chr5:1635400-1638000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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