Variant report

Variant	rs1551559
Chromosome Location	chr19:52034940-52034941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:74)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:74 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr19:52034865-52035197	GM12878	blood:	n/a	n/a
2	USF1	chr19:52034818-52035055	K562	blood:	n/a	n/a
3	RUNX3	chr19:52034772-52035218	GM12878	blood:	n/a	n/a
4	TEAD4	chr19:52034681-52035301	K562	blood:	n/a	n/a
5	MTA3	chr19:52034752-52035275	GM12878	blood:	n/a	n/a
6	EP300	chr19:52034856-52035215	GM12878	blood:	n/a	n/a
7	TBP	chr19:52034860-52035180	K562	blood:	n/a	n/a
8	E2F6	chr19:52034811-52035108	K562	blood:	n/a	n/a
9	RCOR1	chr19:52034938-52035134	GM12878	blood:	n/a	n/a
10	HCFC1	chr19:52034770-52035140	K562	blood:	n/a	n/a
11	ZNF143	chr19:52034766-52035169	K562	blood:	n/a	n/a
12	BCLAF1	chr19:52034760-52035239	GM12878	blood:	n/a	n/a
13	E2F6	chr19:52034772-52035409	K562	blood:	n/a	n/a
14	TBP	chr19:52034831-52035114	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:52034720-52035350	HL-60	blood:	n/a	n/a
16	SPI1	chr19:52034715-52035281	HL-60	blood:	n/a	n/a
17	SPI1	chr19:52034825-52035107	GM12878	blood:	n/a	n/a
18	SPI1	chr19:52034809-52035118	K562	blood:	n/a	n/a
19	MYC	chr19:52034762-52035226	NB4	blood:	n/a	n/a
20	HMGN3	chr19:52034787-52035278	K562	blood:	n/a	n/a
21	EP300	chr19:52034842-52035170	GM12878	blood:	n/a	n/a
22	USF2	chr19:52034813-52035104	GM12878	blood:	n/a	n/a
23	MAX	chr19:52034782-52035249	NB4	blood:	n/a	n/a
24	MAFK	chr19:52034882-52034949	K562	blood:	n/a	n/a
25	POLR2A	chr19:52034751-52035369	GM12891	blood:	n/a	n/a
26	IRF4	chr19:52034715-52035210	GM12878	blood:	n/a	n/a
27	MAX	chr19:52034804-52035225	K562	blood:	n/a	n/a
28	YY1	chr19:52034886-52035237	GM12892	blood:	n/a	n/a
29	CBX3	chr19:52034771-52035172	K562	blood:	n/a	n/a
30	JUND	chr19:52034801-52035235	K562	blood:	n/a	chr19:52035106-52035115
31	TBL1XR1	chr19:52034913-52035113	K562	blood:	n/a	n/a
32	MAX	chr19:52034856-52035121	K562	blood:	n/a	n/a
33	UBTF	chr19:52034743-52035138	K562	blood:	n/a	n/a
34	SPI1	chr19:52034478-52035320	GM12878	blood:	n/a	n/a
35	SPI1	chr19:52034804-52035147	K562	blood:	n/a	n/a
36	EBF1	chr19:52034871-52035218	GM12878	blood:	n/a	n/a
37	REST	chr19:52034883-52035152	Hela-S3	cervix:	n/a	n/a
38	ELF1	chr19:52034704-52035338	GM12878	blood:	n/a	n/a
39	SPI1	chr19:52034713-52035245	GM12891	blood:	n/a	n/a
40	POLR2A	chr19:52034921-52034981	MCF-7	breast:	n/a	n/a
41	MAZ	chr19:52034741-52035228	K562	blood:	n/a	n/a
42	SP1	chr19:52034756-52035127	GM12878	blood:	n/a	chr19:52035104-52035118
43	UBTF	chr19:52034754-52035205	K562	blood:	n/a	n/a
44	SPI1	chr19:52034755-52035195	GM12878	blood:	n/a	n/a
45	BHLHE40	chr19:52034690-52035139	K562	blood:	n/a	n/a
46	SMC3	chr19:52034897-52035058	GM12878	blood:	n/a	n/a
47	POLR2A	chr19:52034857-52035224	K562	blood:	n/a	n/a
48	ZMIZ1	chr19:52034897-52035348	K562	blood:	n/a	n/a
49	MAZ	chr19:52034872-52035141	GM12878	blood:	n/a	n/a
50	RCOR1	chr19:52034765-52035656	K562	blood:	n/a	n/a

No data

Variant related genes	Relation type
SIGLEC6	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10409713	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10410468	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10419617	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10422359	0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.86[ASN][1000 genomes]
rs10853837	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1457098	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2124907	0.90[ASN][1000 genomes]
rs2124909	0.81[CEU][hapmap];0.96[CHB][hapmap];0.96[JPT][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2124910	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2168637	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2290660	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305772	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2864104	0.81[CEU][hapmap]
rs3794986	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4146202	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4146203	0.87[JPT][hapmap]
rs4802800	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4802801	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4802807	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7249285	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7250820	0.81[CEU][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7253637	0.81[CEU][hapmap]
rs7259990	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8100330	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8100538	0.81[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8101887	0.93[ASN][1000 genomes]
rs897783	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];0.97[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1551559	SIGLEC12	cis	lung	GTEx
rs1551559	SIGLEC12	cis	Thyroid	GTEx
rs1551559	SIGLEC12	cis	Artery Tibial	GTEx
rs1551559	SIGLEC12	cis	Esophagus Muscularis	GTEx
rs1551559	SIGLEC12	cis	Adipose Subcutaneous	GTEx
rs1551559	SIGLEC12	cis	Whole Blood	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52032600-52035200	Flanking Active TSS	Placenta	Placenta
2	chr19:52033400-52035600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:52033600-52035600	Flanking Active TSS	Primary B cells from peripheral blood	blood
4	chr19:52034200-52035000	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr19:52034200-52035400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr19:52034200-52035400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
7	chr19:52034200-52035600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr19:52034200-52035600	Enhancers	Primary hematopoietic stem cells	blood
9	chr19:52034400-52035000	Enhancers	GM12878-XiMat	blood
10	chr19:52034400-52035400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
11	chr19:52034600-52035200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:52034600-52035400	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr19:52034600-52035400	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr19:52034600-52035400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:52034600-52035400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:52034600-52035400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr19:52034600-52035400	Enhancers	Spleen	Spleen
18	chr19:52034600-52037600	Enhancers	K562	blood
19	chr19:52034800-52035000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
20	chr19:52034800-52035000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr19:52034800-52035000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:52034800-52035200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
23	chr19:52034800-52035400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
24	chr19:52034800-52035400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr19:52034800-52035600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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