Variant report

Variant	rs12609771
Chromosome Location	chr19:52035182-52035183
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:183)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

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	TEAD4	chr19:52034681-52035301	K562	blood:	n/a	n/a
4	MTA3	chr19:52034752-52035275	GM12878	blood:	n/a	n/a
5	EP300	chr19:52034856-52035215	GM12878	blood:	n/a	n/a
6	BCLAF1	chr19:52034760-52035239	GM12878	blood:	n/a	n/a
7	E2F6	chr19:52034772-52035409	K562	blood:	n/a	n/a
8	POLR2A	chr19:52034720-52035350	HL-60	blood:	n/a	n/a
9	SPI1	chr19:52034715-52035281	HL-60	blood:	n/a	n/a
10	MYC	chr19:52034762-52035226	NB4	blood:	n/a	n/a
11	HMGN3	chr19:52034787-52035278	K562	blood:	n/a	n/a
12	MAX	chr19:52034782-52035249	NB4	blood:	n/a	n/a
13	POLR2A	chr19:52034751-52035369	GM12891	blood:	n/a	n/a
14	IRF4	chr19:52034715-52035210	GM12878	blood:	n/a	n/a
15	MAX	chr19:52034804-52035225	K562	blood:	n/a	n/a
16	YY1	chr19:52034886-52035237	GM12892	blood:	n/a	n/a
17	JUND	chr19:52034801-52035235	K562	blood:	n/a	chr19:52035106-52035115
18	SPI1	chr19:52034478-52035320	GM12878	blood:	n/a	n/a
19	EBF1	chr19:52034871-52035218	GM12878	blood:	n/a	n/a
20	ELF1	chr19:52034704-52035338	GM12878	blood:	n/a	n/a
21	SPI1	chr19:52034713-52035245	GM12891	blood:	n/a	n/a
22	MAZ	chr19:52034741-52035228	K562	blood:	n/a	n/a
23	UBTF	chr19:52034754-52035205	K562	blood:	n/a	n/a
24	SPI1	chr19:52034755-52035195	GM12878	blood:	n/a	n/a
25	POLR2A	chr19:52034857-52035224	K562	blood:	n/a	n/a
26	ZMIZ1	chr19:52034897-52035348	K562	blood:	n/a	n/a
27	RCOR1	chr19:52034765-52035656	K562	blood:	n/a	n/a
28	RUNX3	chr19:52034663-52035433	GM12878	blood:	n/a	n/a
29	REST	chr19:52034801-52035290	HL-60	blood:	n/a	n/a
30	MAX	chr19:52034757-52035199	K562	blood:	n/a	n/a
31	SPI1	chr19:52034666-52035386	HL-60	blood:	n/a	n/a
32	POLR2A	chr19:52034699-52035373	GM18505	blood:	n/a	n/a
33	IRF1	chr19:52034841-52035331	K562	blood:	n/a	chr19:52035171-52035188 chr19:52035172-52035186 chr19:52035173-52035190
34	CCNT2	chr19:52034729-52035197	K562	blood:	n/a	n/a
35	POU2F2	chr19:52034794-52035288	GM12891	blood:	n/a	n/a
36	BCLAF1	chr19:52034809-52035213	GM12878	blood:	n/a	n/a
37	ELF1	chr19:52034756-52035256	GM12878	blood:	n/a	n/a
38	ATF2	chr19:52034816-52035211	GM12878	blood:	n/a	n/a
39	SPI1	chr19:52034718-52035267	GM12891	blood:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:52035161-52035211	NT2-D1	testis:	n/a
2	chr19:52035146-52035196	PrEC	prostate:	n/a
3	chr19:52035146-52035196	AG09319	gingival:	n/a
4	chr19:52035146-52035196	HAEpiC	amniotic membrane:	n/a
5	chr19:52035161-52035211	LNCaP	prostate:	n/a
6	chr19:52035161-52035211	HEEpiC	esophagus:	n/a
7	chr19:52035146-52035196	HRE	kidney:	n/a
8	chr19:52035179-52035229	SK-N-MC	brain:	n/a
9	chr19:52035146-52035196	HCT-116	colon:	n/a
10	chr19:52035179-52035229	HPAEpiC	pulmonary alveolar:	n/a
11	chr19:52035179-52035229	IMR90	lung:	fetal
12	chr19:52035179-52035229	PANC-1	pancreas:	n/a
13	chr19:52035161-52035211	AG04450	lung:	fetal
14	chr19:52035146-52035196	HUVEC	blood vessel:	n/a
15	chr19:52035161-52035211	GM12892	blood:	n/a
16	chr19:52035161-52035211	GM19239	blood:	n/a
17	chr19:52035179-52035229	T-47D	breast:	n/a
18	chr19:52035161-52035211	HRCEpiC	kidney:	n/a
19	chr19:52035146-52035196	PFSK-1	brain:	n/a
20	chr19:52035179-52035229	SK-N-SH	brain:	n/a
21	chr19:52035179-52035229	HRCEpiC	kidney:	n/a
22	chr19:52035146-52035196	HRPEpiC	eye:	n/a
23	chr19:52035161-52035211	AG04449	skin:	fetal
24	chr19:52035161-52035211	AoSMC	blood vessel:	n/a
25	chr19:52035146-52035196	HL-60	blood:	n/a
26	chr19:52035161-52035211	ECC-1	luminal epithelium:	n/a
27	chr19:52035146-52035196	K562	blood:	n/a
28	chr19:52035179-52035229	HRE	kidney:	n/a
29	chr19:52035179-52035229	HCM	heart:	n/a
30	chr19:52035179-52035229	HCF	heart:	n/a
31	chr19:52035146-52035196	NT2-D1	testis:	n/a
32	chr19:52035146-52035196	GM12878	blood:	n/a
33	chr19:52035161-52035211	GM12891	blood:	n/a
34	chr19:52035161-52035211	GM06990	blood:	n/a
35	chr19:52035146-52035196	HCF	heart:	n/a
36	chr19:52035179-52035229	Caco-2	colon:	n/a
37	chr19:52035179-52035229	HepG2	liver:	n/a
38	chr19:52035146-52035196	HEEpiC	esophagus:	n/a
39	chr19:52035179-52035229	HNPCEpiC	eye:	n/a
40	chr19:52035146-52035196	SAEC	small airway:	n/a
41	chr19:52035179-52035229	GM12892	blood:	n/a
42	chr19:52035146-52035196	HEK293	kidney:	embryo
43	chr19:52035146-52035196	AG09309	skin:	n/a
44	chr19:52035146-52035196	NB4	blood:	n/a
45	chr19:52035161-52035211	ProgFib	skin:	n/a
46	chr19:52035146-52035196	ECC-1	luminal epithelium:	n/a
47	chr19:52035161-52035211	HUVEC	blood vessel:	n/a
48	chr19:52035146-52035196	SK-N-SH_RA	brain:	n/a
49	chr19:52035179-52035229	LNCaP	prostate:	n/a
50	chr19:52035146-52035196	SK-N-SH	brain:	n/a

No data

Variant related genes	Relation type
SIGLEC6	TF binding region
SIGLEC6	CpG island

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10221507	0.81[ASN][1000 genomes]
rs11084084	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11084085	0.81[ASN][1000 genomes]
rs12459644	0.93[ASN][1000 genomes]
rs12459648	0.91[ASN][1000 genomes]
rs12459809	0.93[ASN][1000 genomes]
rs12460000	0.91[ASN][1000 genomes]
rs12461762	0.81[ASN][1000 genomes]
rs12461773	0.81[ASN][1000 genomes]
rs12462094	0.90[ASN][1000 genomes]
rs12462104	0.83[ASN][1000 genomes]
rs12463035	0.81[ASN][1000 genomes]
rs12609761	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12609762	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1993462	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2005199	0.81[ASN][1000 genomes]
rs2290659	0.81[ASN][1000 genomes]
rs2290661	0.81[ASN][1000 genomes]
rs2305771	0.83[ASN][1000 genomes]
rs4801875	0.91[ASN][1000 genomes]
rs4802803	0.81[ASN][1000 genomes]
rs4802808	0.93[ASN][1000 genomes]
rs4802809	0.93[ASN][1000 genomes]
rs55985514	0.93[ASN][1000 genomes]
rs56118193	0.93[ASN][1000 genomes]
rs62113284	0.81[ASN][1000 genomes]
rs62113286	0.91[ASN][1000 genomes]
rs62113288	0.91[ASN][1000 genomes]
rs62113289	0.91[ASN][1000 genomes]
rs62116205	0.81[ASN][1000 genomes]
rs73559152	0.81[ASN][1000 genomes]
rs73559183	0.83[ASN][1000 genomes]
rs8105348	0.93[ASN][1000 genomes]
rs8113077	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

No data

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

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links