Variant report

Variant	rs9304717
Chromosome Location	chr19:52010958-52010959
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	TRIM28	chr19:52010920-52011800	K562	blood:	n/a	n/a
3	CEBPB	chr19:52010921-52011724	K562	blood:	n/a	n/a
4	BHLHE40	chr19:52010493-52012020	K562	blood:	n/a	n/a
5	GATA1	chr19:52010857-52011972	PBDE	blood:	n/a	chr19:52011791-52011801 chr19:52011555-52011562 chr19:52011553-52011562 chr19:52011177-52011187
6	ZNF384	chr19:52010443-52011797	K562	blood:	n/a	n/a
7	TAL1	chr19:52010937-52011966	K562	blood:	n/a	n/a
8	MAFF	chr19:52010945-52011643	K562	blood:	n/a	n/a
9	JUND	chr19:52010512-52011828	K562	blood:	n/a	n/a
10	UBTF	chr19:52010786-52012065	K562	blood:	n/a	n/a
11	GATA1	chr19:52009384-52012121	K562	blood:	n/a	chr19:52011791-52011801 chr19:52011555-52011562 chr19:52011553-52011562 chr19:52011177-52011187
12	CEBPB	chr19:52010837-52011736	K562	blood:	n/a	n/a
13	PML	chr19:52010539-52011920	K562	blood:	n/a	n/a
14	PML	chr19:52010894-52011800	K562	blood:	n/a	n/a
15	HMGN3	chr19:52010839-52011855	K562	blood:	n/a	chr19:52011554-52011561
16	MYC	chr19:52010503-52011959	K562	blood:	n/a	chr19:52011273-52011282
17	CEBPD	chr19:52010911-52011846	K562	blood:	n/a	n/a
18	CCNT2	chr19:52010955-52012605	K562	blood:	n/a	n/a
19	EP300	chr19:52010509-52012049	K562	blood:	n/a	n/a
20	ELF1	chr19:52010526-52011351	K562	blood:	n/a	n/a
21	HEY1	chr19:52010931-52011257	K562	blood:	n/a	n/a
22	IRF1	chr19:52010489-52011803	K562	blood:	n/a	chr19:52011192-52011201 chr19:52011686-52011695
23	TEAD4	chr19:52010430-52012129	K562	blood:	n/a	n/a
24	POLR2A	chr19:52010663-52012610	K562	blood:	n/a	n/a
25	NR2F2	chr19:52010568-52012132	K562	blood:	n/a	n/a
26	TBL1XR1	chr19:52010306-52011708	K562	blood:	n/a	n/a
27	NR2F2	chr19:52010537-52011764	K562	blood:	n/a	n/a
28	RCOR1	chr19:52010483-52011796	K562	blood:	n/a	n/a
29	IRF1	chr19:52010571-52011722	K562	blood:	n/a	chr19:52011192-52011201 chr19:52011686-52011695
30	TBL1XR1	chr19:52010888-52011730	K562	blood:	n/a	n/a
31	STAT5A	chr19:52010873-52011804	K562	blood:	n/a	n/a
32	JUN	chr19:52010958-52011706	K562	blood:	n/a	n/a
33	SPI1	chr19:52010865-52011323	K562	blood:	n/a	n/a
34	CUX1	chr19:52010569-52011664	K562	blood:	n/a	n/a
35	MYC	chr19:52010453-52012039	K562	blood:	n/a	chr19:52011273-52011282
36	ZNF143	chr19:52010687-52011530	K562	blood:	n/a	chr19:52011207-52011225
37	SMARCA4	chr19:52010604-52012139	K562	blood:	n/a	n/a
38	MAX	chr19:52010417-52011378	K562	blood:	n/a	chr19:52011273-52011282
39	RCOR1	chr19:52010432-52012002	K562	blood:	n/a	n/a
40	SMARCB1	chr19:52010603-52011998	K562	blood:	n/a	n/a
41	SPI1	chr19:52010867-52011263	K562	blood:	n/a	n/a
42	ZMIZ1	chr19:52010908-52011757	K562	blood:	n/a	n/a
43	TBP	chr19:52010902-52011684	K562	blood:	n/a	n/a
44	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
ENSG00000268839	TF binding region
SIGLEC27P	TF binding region
ENSG00000254521	Chromatin interaction
ENSG00000269388	Chromatin interaction
ENSG00000167765	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

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[ASN][1000 genomes]
rs10421468	1.00[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	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	0.90[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]
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:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9304717	SIGLEC12	cis	Whole Blood	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52002600-52015000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr19:52007800-52011000	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr19:52009400-52011800	Enhancers	Duodenum Mucosa	Duodenum
4	chr19:52009400-52011800	Enhancers	Fetal Intestine Large	intestine
5	chr19:52009400-52012000	Enhancers	Fetal Intestine Small	intestine
6	chr19:52009800-52012400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:52010400-52012200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:52010400-52012400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:52010400-52012600	Flanking Active TSS	K562	blood
10	chr19:52010600-52012000	Enhancers	Stomach Mucosa	stomach
11	chr19:52010800-52011800	Enhancers	Primary hematopoietic stem cells	blood
12	chr19:52010800-52012200	Enhancers	Fetal Muscle Leg	muscle
13	chr19:52010800-52012400	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr19:52010800-52012400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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