Variant report

Variant	rs12609761
Chromosome Location	chr19:52035059-52035060
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:71)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:71 , 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	RUNX3	chr19:52034772-52035218	GM12878	blood:	n/a	n/a
3	MXI1	chr19:52034944-52035130	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	POLR2A	chr19:52034751-52035369	GM12891	blood:	n/a	n/a
25	IRF4	chr19:52034715-52035210	GM12878	blood:	n/a	n/a
26	MAX	chr19:52034804-52035225	K562	blood:	n/a	n/a
27	YY1	chr19:52034886-52035237	GM12892	blood:	n/a	n/a
28	CBX3	chr19:52034771-52035172	K562	blood:	n/a	n/a
29	JUND	chr19:52034801-52035235	K562	blood:	n/a	chr19:52035106-52035115
30	TBL1XR1	chr19:52034913-52035113	K562	blood:	n/a	n/a
31	MAX	chr19:52034856-52035121	K562	blood:	n/a	n/a
32	UBTF	chr19:52034743-52035138	K562	blood:	n/a	n/a
33	SPI1	chr19:52034478-52035320	GM12878	blood:	n/a	n/a
34	SPI1	chr19:52034804-52035147	K562	blood:	n/a	n/a
35	EBF1	chr19:52034871-52035218	GM12878	blood:	n/a	n/a
36	REST	chr19:52034883-52035152	Hela-S3	cervix:	n/a	n/a
37	ELF1	chr19:52034704-52035338	GM12878	blood:	n/a	n/a
38	SPI1	chr19:52034713-52035245	GM12891	blood:	n/a	n/a
39	MAZ	chr19:52034741-52035228	K562	blood:	n/a	n/a
40	SP1	chr19:52034756-52035127	GM12878	blood:	n/a	chr19:52035104-52035118
41	UBTF	chr19:52034754-52035205	K562	blood:	n/a	n/a
42	SPI1	chr19:52034755-52035195	GM12878	blood:	n/a	n/a
43	BHLHE40	chr19:52034690-52035139	K562	blood:	n/a	n/a
44	POLR2A	chr19:52034857-52035224	K562	blood:	n/a	n/a
45	ZMIZ1	chr19:52034897-52035348	K562	blood:	n/a	n/a
46	MAZ	chr19:52034872-52035141	GM12878	blood:	n/a	n/a
47	RCOR1	chr19:52034765-52035656	K562	blood:	n/a	n/a
48	RUNX3	chr19:52034663-52035433	GM12878	blood:	n/a	n/a
49	ZNF143	chr19:52034833-52035081	GM12878	blood:	n/a	n/a
50	REST	chr19:52034801-52035290	HL-60	blood:	n/a	n/a

No data

Variant related genes	Relation type
SIGLEC6	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10221507	0.92[ASN][1000 genomes]
rs11084084	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11084085	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12459644	1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs12459648	0.93[ASN][1000 genomes]
rs12459809	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12460000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12460678	0.89[ASN][1000 genomes]
rs12461433	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12461762	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12461773	0.92[ASN][1000 genomes]
rs12462094	0.91[ASN][1000 genomes]
rs12462104	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12463035	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12609762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12609771	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17239287	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1993462	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2005199	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2290659	0.92[ASN][1000 genomes]
rs2290661	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2305771	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4801872	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[ASN][1000 genomes]
rs4801875	1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4802802	0.89[ASN][1000 genomes]
rs4802803	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4802808	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4802809	0.95[ASN][1000 genomes]
rs55985514	0.95[ASN][1000 genomes]
rs56118193	0.95[ASN][1000 genomes]
rs62113284	0.92[ASN][1000 genomes]
rs62113286	0.93[ASN][1000 genomes]
rs62113288	0.93[ASN][1000 genomes]
rs62113289	0.93[ASN][1000 genomes]
rs62116202	0.89[ASN][1000 genomes]
rs62116203	0.89[ASN][1000 genomes]
rs62116204	0.89[ASN][1000 genomes]
rs62116205	0.92[ASN][1000 genomes]
rs6509546	0.89[JPT][hapmap]
rs73559130	0.89[ASN][1000 genomes]
rs73559152	0.92[ASN][1000 genomes]
rs73559183	0.94[ASN][1000 genomes]
rs8105348	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8106598	0.86[GIH][hapmap]
rs8113077	0.95[ASN][1000 genomes]
rs9807825	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12609761	EPS8L1	cis	parietal	SCAN
rs12609761	ZNF584	cis	cerebellum	SCAN
rs12609761	SIGLEC5	cis	lymphoblastoid	seeQTL

Chromatin state (count:23 , 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	chr19:52034200-52035400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr19:52034200-52035400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
6	chr19:52034200-52035600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr19:52034200-52035600	Enhancers	Primary hematopoietic stem cells	blood
8	chr19:52034400-52035400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
9	chr19:52034600-52035200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:52034600-52035400	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr19:52034600-52035400	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr19:52034600-52035400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:52034600-52035400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:52034600-52035400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr19:52034600-52035400	Enhancers	Spleen	Spleen
16	chr19:52034600-52037600	Enhancers	K562	blood
17	chr19:52034800-52035200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
18	chr19:52034800-52035400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
19	chr19:52034800-52035400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:52034800-52035600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:52035000-52035400	Enhancers	Placenta Amnion	Placenta Amnion
22	chr19:52035000-52035400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr19:52035000-52035600	Flanking Active TSS	GM12878-XiMat	blood

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