Variant report

Variant	rs10419489
Chromosome Location	chr19:52009874-52009875
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	GATA1	chr19:52009384-52012121	K562	blood:	n/a	chr19:52011791-52011801 chr19:52011555-52011562 chr19:52011553-52011562 chr19:52011177-52011187
2	CEBPB	chr19:52009670-52009938	IMR90	lung:	n/a	chr19:52009784-52009795
3	CEBPB	chr19:52009695-52009905	HepG2	liver:	n/a	chr19:52009784-52009795

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52009466..52011500-chr19:52096366..52099744,3	K562	blood:
2	chr19:52004923..52007446-chr19:52009404..52012427,3	K562	blood:

Variant related genes	Relation type
SIGLEC12	TF binding region
ENSG00000268839	TF binding region
SIGLEC27P	TF binding region
ENSG00000167765	Chromatin interaction
ENSG00000254521	Chromatin interaction
ENSG00000269388	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10402495	1.00[ASN][1000 genomes]
rs10421023	1.00[ASN][1000 genomes]
rs10421468	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461323	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12461345	0.97[ASN][1000 genomes]
rs13343377	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2034889	0.95[ASN][1000 genomes]
rs2034891	0.92[ASN][1000 genomes]
rs2864097	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3810105	0.97[ASN][1000 genomes]
rs62116175	0.97[ASN][1000 genomes]
rs62116177	0.97[ASN][1000 genomes]
rs62116178	1.00[ASN][1000 genomes]
rs62116179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509545	0.82[ASN][1000 genomes]
rs7246846	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8106176	0.83[ASN][1000 genomes]
rs8110247	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113414	0.97[ASN][1000 genomes]
rs9304717	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs962129	0.97[ASN][1000 genomes]
rs962130	0.97[ASN][1000 genomes]
rs9676254	1.00[ASN][1000 genomes]
rs9676256	1.00[ASN][1000 genomes]
rs9676266	1.00[ASN][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	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
5	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
6	nsv469584	chr19:52001381-52151821	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv482654	chr19:52001381-52151821	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	esv33175	chr19:52002098-52010839	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10419489	SIGLEC12	cis	Whole Blood	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52002600-52015000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr19:52007000-52010800	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr19:52007800-52011000	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr19:52008200-52010400	Enhancers	K562	blood
5	chr19:52008400-52010800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr19:52009400-52011800	Enhancers	Duodenum Mucosa	Duodenum
7	chr19:52009400-52011800	Enhancers	Fetal Intestine Large	intestine
8	chr19:52009400-52012000	Enhancers	Fetal Intestine Small	intestine
9	chr19:52009800-52012400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links