Variant report

Variant	rs1122493
Chromosome Location	chr19:42133653-42133654
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	SPI1	chr19:42133227-42133804	HL-60	blood:	n/a	chr19:42133444-42133457 chr19:42133514-42133527 chr19:42133552-42133565
2	REST	chr19:42133183-42133697	HL-60	blood:	n/a	chr19:42133473-42133486
3	POLR2A	chr19:42133168-42133774	HL-60	blood:	n/a	n/a

Variant related genes	Relation type
CEACAM4	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs1015758	1.00[CHB][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10407999	0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs10409040	0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs10417599	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417970	0.84[EUR][1000 genomes]
rs10418202	0.83[EUR][1000 genomes]
rs1860328	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016070	0.86[EUR][1000 genomes]
rs2016082	0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs2052080	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2191137	0.85[EUR][1000 genomes]
rs3859459	1.00[CHB][hapmap]
rs3909377	1.00[CHB][hapmap]
rs4090570	1.00[CHB][hapmap]
rs4426458	0.81[EUR][1000 genomes]
rs4802123	1.00[CHB][hapmap]
rs4802126	0.83[EUR][1000 genomes]
rs4803494	0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs4803495	0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs6508988	1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248447	0.85[EUR][1000 genomes]
rs7248956	0.83[EUR][1000 genomes]
rs8106661	0.85[EUR][1000 genomes]
rs8110064	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs887499	1.00[CHB][hapmap]
rs9304598	0.83[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1122493	SCAF1	cis	parietal	SCAN
rs1122493	MYPOP	cis	cerebellum	SCAN
rs1122493	GRIN2D	cis	cerebellum	SCAN
rs1122493	TMEM160	cis	cerebellum	SCAN
rs1122493	IRF3	cis	cerebellum	SCAN
rs1122493	NPAS1	cis	cerebellum	SCAN
rs1122493	GIPR	cis	parietal	SCAN
rs1122493	IL4I1	cis	parietal	SCAN
rs1122493	ZNF229	cis	parietal	SCAN
rs1122493	KCNJ14	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42132000-42133800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
2	chr19:42132400-42134200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:42132600-42133800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr19:42132600-42136800	Weak transcription	Spleen	Spleen
5	chr19:42132800-42133800	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr19:42132800-42134000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:42133200-42134000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr19:42133200-42134200	Enhancers	Pancreas	Pancrea
9	chr19:42133400-42133800	Bivalent Enhancer	Adipose Nuclei	Adipose
10	chr19:42133600-42133800	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr19:42133600-42134200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr19:42133600-42134600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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