Variant report

Variant	rs1015758
Chromosome Location	chr19:42148030-42148031
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:42147475-42149424	A549	lung:	n/a	n/a
2	CTCF	chr19:42147940-42148090	GM12864	blood:	n/a	n/a
3	CTCF	chr19:42147960-42148110	HEK293	kidney:	n/a	n/a
4	CTCF	chr19:42147960-42148110	NHLF	lung:	n/a	n/a
5	CTCF	chr19:42147920-42148070	GM12868	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:42147580..42148927-chr19:42194859..42196377,8	MCF-7	breast:
2	chr12:69104029..69104938-chr19:42147801..42148493,2	MCF-7	breast:
3	chr19:42147964..42148906-chr19:42250000..42251190,4	MCF-7	breast:
4	chr19:42147220..42149633-chr19:42250736..42252324,3	MCF-7	breast:
5	chr19:42148024..42148877-chr19:42195016..42195762,2	K562	blood:
6	chr19:42147995..42149203-chr19:42195085..42195974,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000269354	TF binding region
DNAJC19P3	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10407999	0.95[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10409040	0.89[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs10417599	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417970	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10418202	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1122493	1.00[CHB][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860328	0.87[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016070	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2016082	0.89[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2052080	1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2191137	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3859459	1.00[CHB][hapmap]
rs3909377	1.00[CHB][hapmap]
rs4090570	1.00[CHB][hapmap]
rs4426458	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4802123	1.00[CHB][hapmap]
rs4802126	0.90[EUR][1000 genomes]
rs4803494	0.89[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4803495	0.82[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6508988	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248447	0.91[EUR][1000 genomes]
rs7248956	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8106661	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8110064	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs887499	1.00[CHB][hapmap]
rs9304598	0.90[EUR][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	nsv1057624	chr19:42057334-42152828	Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1058847	chr19:42057334-42172442	Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1063241	chr19:42057334-42175160	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv519408	chr19:42066279-42171906	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3319146	chr19:42082639-42212929	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	esv3319147	chr19:42082742-42212770	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv3422975	chr19:42106166-42212774	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1015758	ZNF229	cis	parietal	SCAN
rs1015758	GIPR	cis	parietal	SCAN
rs1015758	NPAS1	cis	cerebellum	SCAN
rs1015758	KCNJ14	cis	parietal	SCAN
rs1015758	IRF3	cis	cerebellum	SCAN
rs1015758	TMEM160	cis	cerebellum	SCAN
rs1015758	MYPOP	cis	cerebellum	SCAN
rs1015758	SCAF1	cis	parietal	SCAN
rs1015758	GRIN2D	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42143200-42148600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr19:42144400-42148600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr19:42146200-42152600	Weak transcription	Esophagus	oesophagus
4	chr19:42146600-42148800	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr19:42147200-42148800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr19:42148000-42148200	Bivalent Enhancer	Primary B cells from cord blood	blood
7	chr19:42148000-42148200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
8	chr19:42148000-42148400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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