Variant report

Variant	rs1551556
Chromosome Location	chr19:52005669-52005670
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:52005651-52005701	GM12892	blood:	n/a
2	chr19:52005651-52005701	PANC-1	pancreas:	n/a
3	chr19:52005651-52005701	HEK293	kidney:	embryo
4	chr19:52005651-52005701	AG09319	gingival:	n/a
5	chr19:52005651-52005701	GM12891	blood:	n/a
6	chr19:52005651-52005701	AG09309	skin:	n/a
7	chr19:52005651-52005701	HPAEpiC	pulmonary alveolar:	n/a
8	chr19:52005651-52005701	HUVEC	blood vessel:	n/a
9	chr19:52005651-52005701	A549	lung:	n/a
10	chr19:52005651-52005701	NT2-D1	testis:	n/a
11	chr19:52005651-52005701	T-47D	breast:	n/a
12	chr19:52005651-52005701	AoSMC	blood vessel:	n/a
13	chr19:52005651-52005701	HEEpiC	esophagus:	n/a
14	chr19:52005651-52005701	U87	brain:	n/a
15	chr19:52005651-52005701	GM19239	blood:	n/a
16	chr19:52005651-52005701	SK-N-SH_RA	brain:	n/a
17	chr19:52005651-52005701	SK-N-MC	brain:	n/a
18	chr19:52005651-52005701	HAEpiC	amniotic membrane:	n/a
19	chr19:52005651-52005701	PrEC	prostate:	n/a
20	chr19:52005651-52005701	K562	blood:	n/a
21	chr19:52005651-52005701	HNPCEpiC	eye:	n/a
22	chr19:52005651-52005701	HRE	kidney:	n/a
23	chr19:52005651-52005701	HCF	heart:	n/a
24	chr19:52005651-52005701	MCF10A-Er-Src	breast:	n/a
25	chr19:52005651-52005701	AG04449	skin:	fetal
26	chr19:52005651-52005701	AG10803	skin:	n/a
27	chr19:52005651-52005701	GM06990	blood:	n/a
28	chr19:52005651-52005701	HCM	heart:	n/a
29	chr19:52005651-52005701	BJ	skin:	n/a
30	chr19:52005651-52005701	Caco-2	colon:	n/a
31	chr19:52005651-52005701	HepG2	liver:	n/a
32	chr19:52005651-52005701	IMR90	lung:	fetal
33	chr19:52005651-52005701	RPTEC	kidney:	n/a
34	chr19:52005651-52005701	PFSK-1	brain:	n/a
35	chr19:52005651-52005701	ProgFib	skin:	n/a
36	chr19:52005651-52005701	HIPEpiC	eye:	n/a
37	chr19:52005651-52005701	HL-60	blood:	n/a
38	chr19:52005651-52005701	ovcar-3	ovarian:	n/a
39	chr19:52005651-52005701	BE2_C	brain:	n/a
40	chr19:52005651-52005701	AG04450	lung:	fetal
41	chr19:52005651-52005701	NB4	blood:	n/a
42	chr19:52005651-52005701	LNCaP	prostate:	n/a
43	chr19:52005651-52005701	HCT-116	colon:	n/a
44	chr19:52005651-52005701	HMEC	breast:	n/a
45	chr19:52005651-52005701	H1-hESC	embryonic stem cell:	embryo
46	chr19:52005651-52005701	NH-A	brain:	n/a
47	chr19:52005651-52005701	Jurkat	blood:	n/a
48	chr19:52005651-52005701	CMK	blood:	n/a
49	chr19:52005651-52005701	SAEC	small airway:	n/a
50	chr19:52005651-52005701	HRCEpiC	kidney:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:52004923..52007446-chr19:52009404..52012427,3	K562	blood:
2	chr19:52005541..52007329-chr19:52009799..52012427,3	K562	blood:
3	chr19:52005076..52007479-chr19:52052391..52054693,2	K562	blood:
4	chr19:51985395..51986977-chr19:52005149..52007708,2	K562	blood:

No data

Variant related genes	Relation type
SIGLEC12	CpG island
ENSG00000269580	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs10420446	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10420457	0.94[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11084083	0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1160392	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11668941	0.83[EUR][1000 genomes]
rs13343377	0.86[LWK][hapmap];0.86[MEX][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs1551555	0.81[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs16982743	0.83[ASW][hapmap]
rs1973095	0.96[ASN][1000 genomes]
rs2009362	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2864097	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs2864101	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2864102	0.84[CEU][hapmap]
rs2864104	0.84[CEU][hapmap]
rs3810106	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3810108	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810109	0.80[ASN][1000 genomes]
rs3810110	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3810113	0.81[ASN][1000 genomes]
rs3829658	0.82[ASW][hapmap];0.84[CEU][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs3976745	0.87[CEU][hapmap]
rs4801873	0.87[CEU][hapmap]
rs7246846	0.82[MEX][hapmap]
rs7253637	0.84[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs7255948	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8102707	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9304718	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]

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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1551556	SIGLEC12	cis	Whole Blood	GTEx
rs1551556	CXXC4	trans	cerebellum	SCAN
rs1551556	ZNF137P	cis	cerebellum	SCAN
rs1551556	SIGLEC12	cis	Artery Tibial	GTEx
rs1551556	SIGLEC12	cis	lung	GTEx
rs1551556	ZNF584	cis	parietal	SCAN
rs1551556	NLRP5	cis	cerebellum	SCAN
rs1551556	SIGLEC12	cis	Nerve Tibial	GTEx
rs1551556	SIGLEC12	cis	Thyroid	GTEx
rs1551556	SIGLEC12	cis	Artery Aorta	GTEx
rs1551556	DPRX	cis	parietal	SCAN
rs1551556	SIGLEC12	cis	Adipose Subcutaneous	GTEx
rs1551556	ZNF468	cis	cerebellum	SCAN

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	chr19:52004200-52007000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr19:52004200-52007400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:52004400-52006000	Enhancers	K562	blood
5	chr19:52004600-52005800	Enhancers	Primary B cells from cord blood	blood
6	chr19:52004600-52005800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:52004600-52005800	Enhancers	Placenta	Placenta
8	chr19:52004600-52006000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:52004600-52006000	Enhancers	Spleen	Spleen
10	chr19:52005000-52005800	Bivalent Enhancer	Adipose Nuclei	Adipose
11	chr19:52005000-52009400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr19:52005200-52007000	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr19:52005200-52007000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr19:52005200-52007400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links