Variant report

Variant	rs13409154
Chromosome Location	chr2:11889665-11889666
allele	C/G
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	ELF1	chr2:11889276-11889745	GM12878	blood:	n/a	chr2:11889577-11889588
3	MXI1	chr2:11889625-11891607	GM12878	blood:	n/a	chr2:11890697-11890706 chr2:11889929-11889944
4	BHLHE40	chr2:11889642-11891545	GM12878	blood:	n/a	n/a
5	SPI1	chr2:11889412-11889669	GM12891	blood:	n/a	chr2:11889572-11889579 chr2:11889570-11889583 chr2:11889578-11889585 chr2:11889576-11889589 chr2:11889576-11889589
6	RUNX3	chr2:11889612-11891581	GM12878	blood:	n/a	n/a
7	RUNX3	chr2:11889166-11891510	GM12878	blood:	n/a	n/a
8	SPI1	chr2:11889486-11889665	K562	blood:	n/a	chr2:11889572-11889579 chr2:11889570-11889583 chr2:11889578-11889585 chr2:11889576-11889589 chr2:11889576-11889589
9	EP300	chr2:11888661-11891529	GM12878	blood:	n/a	chr2:11889573-11889587 chr2:11889511-11889527 chr2:11889056-11889070 chr2:11889113-11889122
10	WRNIP1	chr2:11887983-11890899	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:11886595-11892488	MCF10A-Er-Src	breast:	n/a	n/a
12	SPI1	chr2:11889484-11889826	HL-60	blood:	n/a	chr2:11889572-11889579 chr2:11889570-11889583 chr2:11889578-11889585 chr2:11889576-11889589 chr2:11889576-11889589
13	TBP	chr2:11889616-11891509	GM12878	blood:	n/a	chr2:11890081-11890092
14	POLR2A	chr2:11889557-11891105	GM12892	blood:	n/a	n/a
15	CHD1	chr2:11886735-11891594	GM12878	blood:	n/a	n/a
16	CHD2	chr2:11888090-11891444	GM12878	blood:	n/a	n/a
17	SPI1	chr2:11889377-11889741	GM12878	blood:	n/a	chr2:11889572-11889579 chr2:11889570-11889583 chr2:11889578-11889585 chr2:11889576-11889589 chr2:11889576-11889589
18	EP300	chr2:11889635-11891585	GM12878	blood:	n/a	n/a
19	POLR2A	chr2:11889153-11891585	GM12878	blood:	n/a	n/a
20	RCOR1	chr2:11888262-11891527	GM12878	blood:	n/a	n/a
21	SPI1	chr2:11889489-11889678	K562	blood:	n/a	chr2:11889572-11889579 chr2:11889570-11889583 chr2:11889578-11889585 chr2:11889576-11889589 chr2:11889576-11889589
22	MAZ	chr2:11888474-11891368	GM12878	blood:	n/a	chr2:11890696-11890706 chr2:11890692-11890707 chr2:11890695-11890706 chr2:11890695-11890705 chr2:11890697-11890706 chr2:11890694-11890709 chr2:11890694-11890707 chr2:11890696-11890705 chr2:11890694-11890707 chr2:11890695-11890706 chr2:11888946-11888956 chr2:11890694-11890707 chr2:11890696-11890705 chr2:11888796-11888806 chr2:11890695-11890706 chr2:11890697-11890704
23	SPI1	chr2:11889111-11890020	GM12878	blood:	n/a	chr2:11889572-11889579 chr2:11889570-11889583 chr2:11889578-11889585 chr2:11889576-11889589 chr2:11889576-11889589
24	POU2F2	chr2:11889158-11891531	GM12878	blood:	n/a	chr2:11890115-11890129 chr2:11890117-11890126 chr2:11891211-11891224 chr2:11890116-11890126 chr2:11890205-11890217 chr2:11890118-11890125 chr2:11890116-11890126 chr2:11890115-11890127
25	POLR2A	chr2:11888404-11891507	GM18505	blood:	n/a	n/a
26	POLR2A	chr2:11889439-11890042	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr2:11889324-11889705	GM12878	blood:	n/a	n/a
28	POLR2A	chr2:11889317-11891423	GM15510	blood:	n/a	n/a
29	MTA3	chr2:11889480-11891467	GM12878	blood:	n/a	n/a
30	POLR2A	chr2:11887260-11891538	GM12891	blood:	n/a	n/a
31	POLR2A	chr2:11888165-11891554	GM12878	blood:	n/a	n/a
32	POLR2A	chr2:11886566-11891563	GM12878	blood:	n/a	n/a
33	MAX	chr2:11889230-11891382	GM12878	blood:	n/a	chr2:11890696-11890706 chr2:11890692-11890707 chr2:11890695-11890706 chr2:11890695-11890705 chr2:11890697-11890706 chr2:11890694-11890709 chr2:11890694-11890707 chr2:11890716-11890726 chr2:11890696-11890705 chr2:11890694-11890707 chr2:11890695-11890706 chr2:11890694-11890707 chr2:11890696-11890705 chr2:11890695-11890706 chr2:11890694-11890704 chr2:11890697-11890704

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11887777..11889810-chr2:11903193..11905347,2	K562	blood:
2	chr2:11827642..11829503-chr2:11889193..11891335,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230790	TF binding region

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

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

rs_ID	r²[population]
rs1006538	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10169802	0.99[ASN][1000 genomes]
rs10192566	0.99[ASN][1000 genomes]
rs10205312	0.89[ASN][1000 genomes]
rs10205400	0.88[ASN][1000 genomes]
rs10207506	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208679	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10209969	0.92[ASN][1000 genomes]
rs11676086	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693809	0.99[ASN][1000 genomes]
rs11897144	0.90[ASN][1000 genomes]
rs13407101	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13412852	0.90[ASN][1000 genomes]
rs1469952	0.84[ASN][1000 genomes]
rs2278513	0.84[ASN][1000 genomes]
rs2358041	0.90[ASN][1000 genomes]
rs2358042	0.90[ASN][1000 genomes]
rs4076055	0.99[ASN][1000 genomes]
rs4315495	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669778	0.83[ASN][1000 genomes]
rs62113306	0.96[ASN][1000 genomes]
rs6717910	0.85[ASN][1000 genomes]
rs6731096	0.96[ASN][1000 genomes]
rs72773994	0.92[ASN][1000 genomes]
rs7595221	0.93[ASN][1000 genomes]
rs873358	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs893342	0.91[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:118 , 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	chr2:11887800-11889800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr2:11887800-11889800	Flanking Active TSS	NHEK	skin
13	chr2:11887800-11890000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:11887800-11891400	Enhancers	Fetal Muscle Leg	muscle
15	chr2:11887800-11894000	Enhancers	Primary B cells from peripheral blood	blood
16	chr2:11888000-11890000	Weak transcription	HSMMtube	muscle
17	chr2:11888000-11890400	Enhancers	Fetal Brain Male	brain
18	chr2:11888000-11891400	Enhancers	Primary B cells from cord blood	blood
19	chr2:11888000-11891600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr2:11888000-11891600	Flanking Active TSS	GM12878-XiMat	blood
21	chr2:11888000-11891800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:11888200-11889800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:11888200-11890000	Flanking Active TSS	NHLF	lung
24	chr2:11888200-11890600	Weak transcription	Osteobl	bone
25	chr2:11888200-11891200	Enhancers	Brain Cingulate Gyrus	brain
26	chr2:11888200-11891400	Enhancers	Brain Angular Gyrus	brain
27	chr2:11888400-11889800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:11888400-11889800	Enhancers	Gastric	stomach
29	chr2:11888400-11890000	Enhancers	Liver	Liver
30	chr2:11888400-11890200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:11888400-11890200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr2:11888400-11890400	Enhancers	Lung	lung
33	chr2:11888400-11890600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr2:11888400-11890600	Enhancers	Adipose Nuclei	Adipose
35	chr2:11888400-11890600	Enhancers	Brain Germinal Matrix	brain
36	chr2:11888400-11890800	Weak transcription	Placenta	Placenta
37	chr2:11888400-11890800	Enhancers	Ovary	ovary
38	chr2:11888400-11891000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:11888400-11891000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:11888400-11891200	Enhancers	Brain Substantia Nigra	brain
41	chr2:11888400-11891400	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr2:11888400-11891400	Enhancers	Left Ventricle	heart
43	chr2:11888400-11891400	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr2:11888400-11891600	Enhancers	Fetal Thymus	thymus
45	chr2:11888400-11891600	Enhancers	Dnd41	blood
46	chr2:11888400-11891800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:11888400-11893000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:11888400-11893200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr2:11888400-11893600	Weak transcription	HSMM	muscle
50	chr2:11888400-11895000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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