Variant report

Variant	rs9304718
Chromosome Location	chr19:52011930-52011931
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	GATA1	chr19:52010857-52011972	PBDE	blood:	n/a	chr19:52011791-52011801 chr19:52011555-52011562 chr19:52011553-52011562 chr19:52011177-52011187
4	TAL1	chr19:52010937-52011966	K562	blood:	n/a	n/a
5	ELF1	chr19:52011376-52011953	K562	blood:	n/a	chr19:52011898-52011909
6	UBTF	chr19:52010786-52012065	K562	blood:	n/a	n/a
7	GATA1	chr19:52009384-52012121	K562	blood:	n/a	chr19:52011791-52011801 chr19:52011555-52011562 chr19:52011553-52011562 chr19:52011177-52011187
8	MYC	chr19:52010503-52011959	K562	blood:	n/a	chr19:52011273-52011282
9	CCNT2	chr19:52010955-52012605	K562	blood:	n/a	n/a
10	EP300	chr19:52010509-52012049	K562	blood:	n/a	n/a
11	MAX	chr19:52011397-52012034	K562	blood:	n/a	n/a
12	SPI1	chr19:52011680-52012066	HL-60	blood:	n/a	n/a
13	TEAD4	chr19:52010430-52012129	K562	blood:	n/a	n/a
14	POLR2A	chr19:52010663-52012610	K562	blood:	n/a	n/a
15	NR2F2	chr19:52010568-52012132	K562	blood:	n/a	n/a
16	NFYB	chr19:52011032-52012063	K562	blood:	n/a	n/a
17	MYC	chr19:52010453-52012039	K562	blood:	n/a	chr19:52011273-52011282
18	SMARCA4	chr19:52010604-52012139	K562	blood:	n/a	n/a
19	SPI1	chr19:52011756-52012036	K562	blood:	n/a	n/a
20	RCOR1	chr19:52010432-52012002	K562	blood:	n/a	n/a
21	SMARCB1	chr19:52010603-52011998	K562	blood:	n/a	n/a
22	CBX3	chr19:52010361-52012240	K562	blood:	n/a	n/a

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CEACAM18-3	chr19:52011827-52012121	NONHSAT067446
2	lnc-CEACAM18-3	chr19:52011827-52012108	NONHSAT067447

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

Extended variants
information (count: 32 )
Associated
traits (count: 17 )

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

rs_ID	r²[population]
rs10420446	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10420457	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11084083	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1160392	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668941	0.83[EUR][1000 genomes]
rs13343377	0.86[MEX][hapmap]
rs1551555	0.83[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs1551556	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1973095	0.97[ASN][1000 genomes]
rs2009362	0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2864101	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864102	0.84[CEU][hapmap]
rs2864104	0.84[CEU][hapmap]
rs3810106	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3810108	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3810109	0.81[ASN][1000 genomes]
rs3810110	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3810113	0.81[ASN][1000 genomes]
rs3829658	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs3976745	0.87[CEU][hapmap]
rs4801873	0.87[CEU][hapmap]
rs7246846	0.87[LWK][hapmap];0.82[MEX][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs7253637	0.84[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs7255948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8102707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs9304718	ZNF137P	cis	cerebellum	SCAN
rs9304718	NLRP5	cis	cerebellum	SCAN
rs9304718	SIGLEC12	cis	Thyroid	GTEx
rs9304718	SIGLEC12	cis	Nerve Tibial	GTEx
rs9304718	SIGLEC5	cis	lymphoblastoid	seeQTL
rs9304718	SIGLEC12	cis	multi-tissue	Pritchard
rs9304718	SIGLEC12	cis	Liver	GTEx
rs9304718	SIGLEC12	cis	Adipose Subcutaneous	GTEx
rs9304718	C20orf194	cis	Liver	GTEx
rs9304718	ZNF584	cis	parietal	SCAN
rs9304718	SIGLEC12	cis	lung	GTEx
rs9304718	SIGLEC12	cis	Artery Aorta	GTEx
rs9304718	SIGLEC12	cis	Artery Tibial	GTEx
rs9304718	SIGLEC12	cis	Whole Blood	GTEx
rs9304718	SIGLEC10	cis	multi-tissue	Pritchard
rs9304718	C20orf194	trans	multi-tissue	Pritchard
rs9304718	ZNF468	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52002600-52015000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr19:52009400-52012000	Enhancers	Fetal Intestine Small	intestine
3	chr19:52009800-52012400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:52010400-52012200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:52010400-52012400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:52010400-52012600	Flanking Active TSS	K562	blood
7	chr19:52010600-52012000	Enhancers	Stomach Mucosa	stomach
8	chr19:52010800-52012200	Enhancers	Fetal Muscle Leg	muscle
9	chr19:52010800-52012400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr19:52010800-52012400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr19:52011600-52012200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr19:52011600-52012400	Enhancers	Primary B cells from cord blood	blood
13	chr19:52011800-52012000	Bivalent Enhancer	Adipose Nuclei	Adipose
14	chr19:52011800-52013000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr19:52011800-52013200	Weak transcription	Fetal Intestine Large	intestine

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