Variant report

Variant	rs10421468
Chromosome Location	chr19:52010727-52010728
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	MAZ	chr19:52010625-52012202	K562	blood:	n/a	chr19:52011273-52011282
2	BHLHE40	chr19:52010493-52012020	K562	blood:	n/a	n/a
3	ZNF384	chr19:52010443-52011797	K562	blood:	n/a	n/a
4	JUND	chr19:52010512-52011828	K562	blood:	n/a	n/a
5	GATA1	chr19:52009384-52012121	K562	blood:	n/a	chr19:52011791-52011801 chr19:52011555-52011562 chr19:52011553-52011562 chr19:52011177-52011187
6	PML	chr19:52010539-52011920	K562	blood:	n/a	n/a
7	MYC	chr19:52010503-52011959	K562	blood:	n/a	chr19:52011273-52011282
8	EP300	chr19:52010509-52012049	K562	blood:	n/a	n/a
9	ELF1	chr19:52010526-52011351	K562	blood:	n/a	n/a
10	IRF1	chr19:52010489-52011803	K562	blood:	n/a	chr19:52011192-52011201 chr19:52011686-52011695
11	TEAD4	chr19:52010430-52012129	K562	blood:	n/a	n/a
12	POLR2A	chr19:52010663-52012610	K562	blood:	n/a	n/a
13	NR2F2	chr19:52010568-52012132	K562	blood:	n/a	n/a
14	TBL1XR1	chr19:52010306-52011708	K562	blood:	n/a	n/a
15	NR2F2	chr19:52010537-52011764	K562	blood:	n/a	n/a
16	RCOR1	chr19:52010483-52011796	K562	blood:	n/a	n/a
17	IRF1	chr19:52010571-52011722	K562	blood:	n/a	chr19:52011192-52011201 chr19:52011686-52011695
18	CUX1	chr19:52010569-52011664	K562	blood:	n/a	n/a
19	MYC	chr19:52010453-52012039	K562	blood:	n/a	chr19:52011273-52011282
20	ZNF143	chr19:52010687-52011530	K562	blood:	n/a	chr19:52011207-52011225
21	POLR2A	chr19:52010620-52010789	K562	blood:	n/a	n/a
22	SMARCA4	chr19:52010604-52012139	K562	blood:	n/a	n/a
23	MAX	chr19:52010417-52011378	K562	blood:	n/a	chr19:52011273-52011282
24	RCOR1	chr19:52010432-52012002	K562	blood:	n/a	n/a
25	SMARCB1	chr19:52010603-52011998	K562	blood:	n/a	n/a
26	CBX3	chr19:52010361-52012240	K562	blood:	n/a	n/a

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
SIGLEC27P	TF binding region
ENSG00000268839	TF binding region
ENSG00000167765	Chromatin interaction
ENSG00000269388	Chromatin interaction
ENSG00000254521	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10402495	1.00[ASN][1000 genomes]
rs10419489	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421023	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12461323	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12461345	0.97[ASN][1000 genomes]
rs12463300	0.90[JPT][hapmap]
rs13343377	0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2034889	0.95[ASN][1000 genomes]
rs2034891	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2864097	0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3810105	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs62116175	0.97[ASN][1000 genomes]
rs62116177	0.97[ASN][1000 genomes]
rs62116178	1.00[ASN][1000 genomes]
rs62116179	0.98[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	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8106176	0.83[ASN][1000 genomes]
rs8110247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113414	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9304717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs962129	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs962130	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9676254	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9676256	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9676266	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9676272	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]

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
rs10421468	SIGLEC12	cis	Whole Blood	GTEx

Chromatin state (count:12 , 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	chr19:52008400-52010800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr19:52009400-52011800	Enhancers	Duodenum Mucosa	Duodenum
6	chr19:52009400-52011800	Enhancers	Fetal Intestine Large	intestine
7	chr19:52009400-52012000	Enhancers	Fetal Intestine Small	intestine
8	chr19:52009800-52012400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:52010400-52012200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:52010400-52012400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:52010400-52012600	Flanking Active TSS	K562	blood
12	chr19:52010600-52012000	Enhancers	Stomach Mucosa	stomach

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