Variant report

Variant	rs11693809
Chromosome Location	chr2:11890138-11890139
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	POLR2A	chr2:11886620-11891581	GM12878	blood:	n/a	n/a
2	BATF	chr2:11889954-11890298	GM12878	blood:	n/a	n/a
3	FOXM1	chr2:11889802-11891015	GM12878	blood:	n/a	chr2:11889882-11889890
4	MXI1	chr2:11889625-11891607	GM12878	blood:	n/a	chr2:11890697-11890706 chr2:11889929-11889944
5	BCLAF1	chr2:11889811-11890456	GM12878	blood:	n/a	n/a
6	FOXM1	chr2:11889830-11891135	GM12878	blood:	n/a	chr2:11889882-11889890
7	RELA	chr2:11889671-11891397	GM18505	blood:	n/a	chr2:11890035-11890044 chr2:11890035-11890044
8	PML	chr2:11889757-11891316	GM12878	blood:	n/a	chr2:11889904-11889912
9	BHLHE40	chr2:11889642-11891545	GM12878	blood:	n/a	n/a
10	RELA	chr2:11889833-11890926	GM18951	blood:	n/a	chr2:11890035-11890044 chr2:11890035-11890044
11	EBF1	chr2:11889912-11890599	GM12878	blood:	n/a	n/a
12	NFATC1	chr2:11889851-11890381	GM12878	blood:	n/a	n/a
13	RUNX3	chr2:11889612-11891581	GM12878	blood:	n/a	n/a
14	EP300	chr2:11889962-11890359	GM12878	blood:	n/a	n/a
15	CREB1	chr2:11889792-11891364	GM12878	blood:	n/a	n/a
16	STAT1	chr2:11889829-11890936	GM12878	blood:	n/a	chr2:11890206-11890218 chr2:11890207-11890219
17	RUNX3	chr2:11889166-11891510	GM12878	blood:	n/a	n/a
18	SIN3A	chr2:11889678-11891474	GM12878	blood:	n/a	n/a
19	IKZF1	chr2:11889708-11891443	GM12878	blood:	n/a	n/a
20	FOS	chr2:11890104-11890179	MCF10A-Er-Src	breast:	n/a	n/a
21	EP300	chr2:11888661-11891529	GM12878	blood:	n/a	chr2:11889573-11889587 chr2:11889511-11889527 chr2:11889056-11889070 chr2:11889113-11889122
22	PML	chr2:11890007-11890259	GM12878	blood:	n/a	n/a
23	ZNF143	chr2:11889880-11890874	GM12878	blood:	n/a	n/a
24	WRNIP1	chr2:11887983-11890899	GM12878	blood:	n/a	n/a
25	MTA3	chr2:11890097-11890938	GM12878	blood:	n/a	n/a
26	ATF2	chr2:11889831-11890411	GM12878	blood:	n/a	n/a
27	ZNF384	chr2:11889876-11890229	GM12878	blood:	n/a	n/a
28	PAX5	chr2:11889833-11890291	GM12878	blood:	n/a	n/a
29	SP1	chr2:11889876-11890408	GM12878	blood:	n/a	chr2:11890204-11890216 chr2:11890206-11890215 chr2:11890211-11890220 chr2:11890205-11890219
30	ZEB1	chr2:11890000-11890457	GM12878	blood:	n/a	n/a
31	TCF3	chr2:11890020-11890317	GM12878	blood:	n/a	n/a
32	POLR2A	chr2:11886595-11892488	MCF10A-Er-Src	breast:	n/a	n/a
33	TBP	chr2:11889616-11891509	GM12878	blood:	n/a	chr2:11890081-11890092
34	POLR2A	chr2:11889557-11891105	GM12892	blood:	n/a	n/a
35	EBF1	chr2:11890034-11890307	GM12878	blood:	n/a	n/a
36	STAT5A	chr2:11889881-11890469	GM12878	blood:	n/a	chr2:11890206-11890218 chr2:11890207-11890219
37	CHD1	chr2:11886735-11891594	GM12878	blood:	n/a	n/a
38	STAT5A	chr2:11889788-11890455	GM12878	blood:	n/a	chr2:11890206-11890218 chr2:11890207-11890219
39	NFYB	chr2:11889881-11890222	GM12878	blood:	n/a	n/a
40	BCLAF1	chr2:11889674-11890399	GM12878	blood:	n/a	n/a
41	RELA	chr2:11889825-11890244	GM19193	blood:	n/a	chr2:11890035-11890044 chr2:11890035-11890044
42	CREB1	chr2:11889824-11891508	GM12878	blood:	n/a	n/a
43	BCL11A	chr2:11889970-11890340	GM12878	blood:	n/a	n/a
44	POLR2A	chr2:11889740-11890540	GM12878	blood:	n/a	n/a
45	CHD2	chr2:11888090-11891444	GM12878	blood:	n/a	n/a
46	TBL1XR1	chr2:11889759-11891516	GM12878	blood:	n/a	n/a
47	CEBPB	chr2:11889667-11891002	GM12878	blood:	n/a	n/a
48	EP300	chr2:11889635-11891585	GM12878	blood:	n/a	n/a
49	RFX5	chr2:11889826-11890213	GM12878	blood:	n/a	chr2:11889930-11889945
50	MEF2C	chr2:11889789-11891401	GM12878	blood:	n/a	chr2:11890041-11890055

No.	Distal block	Cell Line	Cell type
1	chr2:11886726..11888240-chr2:11889703..11892013,2	MCF-7	breast:
2	chr2:11827642..11829503-chr2:11889193..11891335,2	MCF-7	breast:
3	chr2:11890007..11892295-chr2:11917973..11920590,2	K562	blood:

Variant related genes	Relation type
ENSG00000230790	TF binding region
ENSG00000134324	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1006538	0.91[ASN][1000 genomes]
rs10169802	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10192566	1.00[ASN][1000 genomes]
rs10205312	0.90[ASN][1000 genomes]
rs10205400	0.89[ASN][1000 genomes]
rs10207506	0.99[ASN][1000 genomes]
rs10208679	0.99[ASN][1000 genomes]
rs10209969	0.91[ASN][1000 genomes]
rs11676086	0.99[ASN][1000 genomes]
rs11897144	0.91[ASN][1000 genomes]
rs13407101	0.93[ASN][1000 genomes]
rs13409154	0.99[ASN][1000 genomes]
rs13412852	0.89[ASN][1000 genomes]
rs1469952	0.85[ASN][1000 genomes]
rs2278513	0.85[ASN][1000 genomes]
rs2358041	0.89[ASN][1000 genomes]
rs2358042	0.89[ASN][1000 genomes]
rs4076055	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4315495	0.99[ASN][1000 genomes]
rs4669778	0.82[ASN][1000 genomes]
rs62113306	0.97[ASN][1000 genomes]
rs6717910	0.84[ASN][1000 genomes]
rs6731096	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs72773994	0.91[ASN][1000 genomes]
rs7595221	0.94[ASN][1000 genomes]
rs873358	0.99[ASN][1000 genomes]
rs893342	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
4	nsv580973	chr2:11864946-11898931	Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv580974	chr2:11867841-11898931	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11887000-11890400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:11887000-11891600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:11887200-11890400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr2:11887400-11890400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:11887400-11890400	Enhancers	Spleen	Spleen
6	chr2:11887400-11890600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr2:11887600-11890400	Enhancers	Fetal Muscle Trunk	muscle
8	chr2:11887600-11890600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:11887600-11891200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr2:11887600-11891400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:11887800-11891400	Enhancers	Fetal Muscle Leg	muscle
12	chr2:11887800-11894000	Enhancers	Primary B cells from peripheral blood	blood
13	chr2:11888000-11890400	Enhancers	Fetal Brain Male	brain
14	chr2:11888000-11891400	Enhancers	Primary B cells from cord blood	blood
15	chr2:11888000-11891600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr2:11888000-11891600	Flanking Active TSS	GM12878-XiMat	blood
17	chr2:11888000-11891800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:11888200-11890600	Weak transcription	Osteobl	bone
19	chr2:11888200-11891200	Enhancers	Brain Cingulate Gyrus	brain
20	chr2:11888200-11891400	Enhancers	Brain Angular Gyrus	brain
21	chr2:11888400-11890200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:11888400-11890200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr2:11888400-11890400	Enhancers	Lung	lung
24	chr2:11888400-11890600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:11888400-11890600	Enhancers	Adipose Nuclei	Adipose
26	chr2:11888400-11890600	Enhancers	Brain Germinal Matrix	brain
27	chr2:11888400-11890800	Weak transcription	Placenta	Placenta
28	chr2:11888400-11890800	Enhancers	Ovary	ovary
29	chr2:11888400-11891000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:11888400-11891000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:11888400-11891200	Enhancers	Brain Substantia Nigra	brain
32	chr2:11888400-11891400	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr2:11888400-11891400	Enhancers	Left Ventricle	heart
34	chr2:11888400-11891400	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr2:11888400-11891600	Enhancers	Fetal Thymus	thymus
36	chr2:11888400-11891600	Enhancers	Dnd41	blood
37	chr2:11888400-11891800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:11888400-11893000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:11888400-11893200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr2:11888400-11893600	Weak transcription	HSMM	muscle
41	chr2:11888400-11895000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:11888400-11916400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr2:11888600-11890400	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr2:11888600-11890400	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr2:11888600-11890400	Enhancers	Right Atrium	heart
46	chr2:11888600-11890600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr2:11888600-11890600	Enhancers	Fetal Brain Female	brain
48	chr2:11888600-11890800	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr2:11888600-11890800	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr2:11888600-11890800	Enhancers	Skeletal Muscle Female	skeletal muscle

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