Variant report

Variant	rs4803520
Chromosome Location	chr19:42500373-42500374
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	RFX5	chr19:42499835-42503184	SK-N-SH	brain:	n/a	chr19:42500315-42500323 chr19:42500255-42500270 chr19:42500254-42500271 chr19:42500257-42500272 chr19:42500317-42500326 chr19:42500316-42500331 chr19:42500316-42500331 chr19:42500316-42500331 chr19:42500315-42500332 chr19:42500256-42500265 chr19:42500253-42500267 chr19:42500255-42500270 chr19:42500255-42500270 chr19:42500314-42500328 chr19:42501847-42501862
2	ZBTB7A	chr19:42500197-42500523	K562	blood:	n/a	n/a
3	REST	chr19:42499691-42501939	SK-N-SH	brain:	n/a	chr19:42501256-42501269 chr19:42501438-42501447 chr19:42500483-42500492 chr19:42501428-42501446
4	RCOR1	chr19:42500101-42500435	K562	blood:	n/a	n/a
5	SIN3A	chr19:42500112-42500475	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr19:42497259-42501389	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr19:42499326-42502337	H1-neurons	neurons:	n/a	n/a
8	MXI1	chr19:42499822-42504557	SK-N-SH	brain:	n/a	chr19:42500254-42500269 chr19:42500315-42500330 chr19:42500256-42500271 chr19:42500317-42500332 chr19:42501846-42501861
9	REST	chr19:42499838-42500373	PFSK-1	brain:	n/a	n/a
10	MXI1	chr19:42500114-42500432	H1-hESC	embryonic stem cell:	n/a	chr19:42500254-42500269 chr19:42500315-42500330 chr19:42500256-42500271 chr19:42500317-42500332
11	REST	chr19:42500094-42500736	H1-hESC	embryonic stem cell:	n/a	chr19:42500483-42500492
12	EP300	chr19:42499667-42503165	SK-N-SH	brain:	n/a	chr19:42500027-42500040 chr19:42501978-42501992 chr19:42499723-42499730 chr19:42502309-42502325
13	MAX	chr19:42500103-42500455	H1-hESC	embryonic stem cell:	n/a	chr19:42500317-42500326 chr19:42500321-42500330 chr19:42500260-42500269 chr19:42500256-42500265
14	REST	chr19:42498991-42501889	A549	lung:	n/a	chr19:42501256-42501269 chr19:42501438-42501447 chr19:42500483-42500492 chr19:42501428-42501446
15	REST	chr19:42499978-42501095	H1-neurons	neurons:	n/a	chr19:42500483-42500492
16	RFX5	chr19:42500093-42500503	H1-hESC	embryonic stem cell:	n/a	chr19:42500315-42500323 chr19:42500255-42500270 chr19:42500254-42500271 chr19:42500257-42500272 chr19:42500317-42500326 chr19:42500316-42500331 chr19:42500316-42500331 chr19:42500316-42500331 chr19:42500315-42500332 chr19:42500256-42500265 chr19:42500253-42500267 chr19:42500255-42500270 chr19:42500255-42500270 chr19:42500314-42500328
17	REST	chr19:42500047-42500459	SK-N-SH	brain:	n/a	n/a
18	SP1	chr19:42499967-42500462	H1-hESC	embryonic stem cell:	n/a	chr19:42500337-42500349 chr19:42500334-42500348 chr19:42500337-42500349
19	REST	chr19:42499919-42503116	HL-60	blood:	n/a	chr19:42501256-42501269 chr19:42501438-42501447 chr19:42500483-42500492 chr19:42501428-42501446
20	MXI1	chr19:42500165-42500458	K562	blood:	n/a	chr19:42500254-42500269 chr19:42500315-42500330 chr19:42500256-42500271 chr19:42500317-42500332
21	REST	chr19:42500169-42500381	H1-hESC	embryonic stem cell:	n/a	n/a
22	REST	chr19:42500033-42501945	ECC-1	luminal epithelium:	n/a	chr19:42501256-42501269 chr19:42501438-42501447 chr19:42500483-42500492 chr19:42501428-42501446
23	RCOR1	chr19:42500060-42500489	K562	blood:	n/a	n/a
24	REST	chr19:42500079-42501927	K562	blood:	n/a	chr19:42501256-42501269 chr19:42501438-42501447 chr19:42500483-42500492 chr19:42501428-42501446
25	REST	chr19:42499564-42502009	H1-neurons	neurons:	n/a	chr19:42501256-42501269 chr19:42501438-42501447 chr19:42500483-42500492 chr19:42501428-42501446

No.	Distal block	Cell Line	Cell type
1	chr19:42385208..42386943-chr19:42498779..42500778,2	K562	blood:
2	chr19:42499288..42501034-chr19:42524596..42527104,2	K562	blood:
3	chr19:42499152..42501127-chr19:42507187..42509565,3	MCF-7	breast:

Variant related genes	Relation type
ATP1A3	TF binding region
ENSG00000105737	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10407506	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs10500285	1.00[ASW][hapmap];0.93[CHD][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap]
rs11880124	0.91[TSI][hapmap]
rs11883412	0.96[TSI][hapmap]
rs16975663	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs17270169	0.90[CEU][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs17342284	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs2217342	0.83[GIH][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs3736109	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3826705	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs407096	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443239	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454150	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251466	1.00[ASW][hapmap];0.90[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs899661	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
5	nsv911780	chr19:42398450-42521108	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv911781	chr19:42398450-42542999	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4803520	ZNF219	trans	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42498000-42503800	Enhancers	Fetal Brain Male	brain
2	chr19:42498600-42501200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:42498600-42507600	Weak transcription	Right Atrium	heart
4	chr19:42498800-42502800	Flanking Active TSS	Fetal Brain Female	brain
5	chr19:42499200-42500600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr19:42499200-42501000	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
7	chr19:42499600-42500600	Weak transcription	Dnd41	blood
8	chr19:42499600-42501000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:42499600-42501200	Flanking Active TSS	Brain Germinal Matrix	brain
10	chr19:42499600-42501400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:42500000-42501400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr19:42500200-42500800	Enhancers	Brain Angular Gyrus	brain

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