Variant report

Variant	rs4076516
Chromosome Location	chr2:11889529-11889530
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	ELF1	chr2:11889276-11889745	GM12878	blood:	n/a	chr2:11889577-11889588
3	EBF1	chr2:11889240-11889534	GM12878	blood:	n/a	n/a
4	SPI1	chr2:11889412-11889669	GM12891	blood:	n/a	chr2:11889572-11889579 chr2:11889570-11889583 chr2:11889578-11889585 chr2:11889576-11889589 chr2:11889576-11889589
5	RUNX3	chr2:11889166-11891510	GM12878	blood:	n/a	n/a
6	SPI1	chr2:11889486-11889665	K562	blood:	n/a	chr2:11889572-11889579 chr2:11889570-11889583 chr2:11889578-11889585 chr2:11889576-11889589 chr2:11889576-11889589
7	EP300	chr2:11888661-11891529	GM12878	blood:	n/a	chr2:11889573-11889587 chr2:11889511-11889527 chr2:11889056-11889070 chr2:11889113-11889122
8	WRNIP1	chr2:11887983-11890899	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:11886595-11892488	MCF10A-Er-Src	breast:	n/a	n/a
10	SPI1	chr2:11889484-11889826	HL-60	blood:	n/a	chr2:11889572-11889579 chr2:11889570-11889583 chr2:11889578-11889585 chr2:11889576-11889589 chr2:11889576-11889589
11	CTCF	chr2:11889420-11889570	GM12874	blood:	n/a	n/a
12	CHD1	chr2:11886735-11891594	GM12878	blood:	n/a	n/a
13	CHD2	chr2:11888090-11891444	GM12878	blood:	n/a	n/a
14	SPI1	chr2:11889377-11889741	GM12878	blood:	n/a	chr2:11889572-11889579 chr2:11889570-11889583 chr2:11889578-11889585 chr2:11889576-11889589 chr2:11889576-11889589
15	ZBTB7A	chr2:11889374-11889551	K562	blood:	n/a	n/a
16	POLR2A	chr2:11889153-11891585	GM12878	blood:	n/a	n/a
17	RCOR1	chr2:11888262-11891527	GM12878	blood:	n/a	n/a
18	SPI1	chr2:11889489-11889678	K562	blood:	n/a	chr2:11889572-11889579 chr2:11889570-11889583 chr2:11889578-11889585 chr2:11889576-11889589 chr2:11889576-11889589
19	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
20	SPI1	chr2:11889111-11890020	GM12878	blood:	n/a	chr2:11889572-11889579 chr2:11889570-11889583 chr2:11889578-11889585 chr2:11889576-11889589 chr2:11889576-11889589
21	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
22	POLR2A	chr2:11888404-11891507	GM18505	blood:	n/a	n/a
23	POLR2A	chr2:11889439-11890042	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr2:11889324-11889705	GM12878	blood:	n/a	n/a
25	POLR2A	chr2:11889317-11891423	GM15510	blood:	n/a	n/a
26	MTA3	chr2:11889480-11891467	GM12878	blood:	n/a	n/a
27	POLR2A	chr2:11889241-11889609	K562	blood:	n/a	n/a
28	POLR2A	chr2:11887260-11891538	GM12891	blood:	n/a	n/a
29	POLR2A	chr2:11888165-11891554	GM12878	blood:	n/a	n/a
30	POLR2A	chr2:11886566-11891563	GM12878	blood:	n/a	n/a
31	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: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs16855583	0.90[AFR][1000 genomes]
rs16857840	0.90[AFR][1000 genomes]
rs16857843	0.95[AFR][1000 genomes]
rs73181399	0.88[AFR][1000 genomes]
rs73183104	0.83[AFR][1000 genomes]
rs73183109	0.88[AFR][1000 genomes]
rs73183116	0.93[AFR][1000 genomes]
rs73183118	0.93[AFR][1000 genomes]
rs73183119	0.93[AFR][1000 genomes]
rs73183121	0.93[AFR][1000 genomes]
rs73185104	0.90[AFR][1000 genomes]
rs871674	0.95[AFR][1000 genomes]
rs893351	0.93[AFR][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	chr2:11887400-11889600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:11887400-11889600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:11887400-11890400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:11887400-11890400	Enhancers	Spleen	Spleen
8	chr2:11887400-11890600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr2:11887600-11890400	Enhancers	Fetal Muscle Trunk	muscle
10	chr2:11887600-11890600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:11887600-11891200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr2:11887600-11891400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:11887800-11889600	Flanking Active TSS	HepG2	liver
14	chr2:11887800-11889800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:11887800-11889800	Flanking Active TSS	NHEK	skin
16	chr2:11887800-11890000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:11887800-11891400	Enhancers	Fetal Muscle Leg	muscle
18	chr2:11887800-11894000	Enhancers	Primary B cells from peripheral blood	blood
19	chr2:11888000-11889600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:11888000-11889600	Flanking Active TSS	Right Ventricle	heart
21	chr2:11888000-11890000	Weak transcription	HSMMtube	muscle
22	chr2:11888000-11890400	Enhancers	Fetal Brain Male	brain
23	chr2:11888000-11891400	Enhancers	Primary B cells from cord blood	blood
24	chr2:11888000-11891600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr2:11888000-11891600	Flanking Active TSS	GM12878-XiMat	blood
26	chr2:11888000-11891800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:11888200-11889800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:11888200-11890000	Flanking Active TSS	NHLF	lung
29	chr2:11888200-11890600	Weak transcription	Osteobl	bone
30	chr2:11888200-11891200	Enhancers	Brain Cingulate Gyrus	brain
31	chr2:11888200-11891400	Enhancers	Brain Angular Gyrus	brain
32	chr2:11888400-11889600	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr2:11888400-11889800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:11888400-11889800	Enhancers	Gastric	stomach
35	chr2:11888400-11890000	Enhancers	Liver	Liver
36	chr2:11888400-11890200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:11888400-11890200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr2:11888400-11890400	Enhancers	Lung	lung
39	chr2:11888400-11890600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr2:11888400-11890600	Enhancers	Adipose Nuclei	Adipose
41	chr2:11888400-11890600	Enhancers	Brain Germinal Matrix	brain
42	chr2:11888400-11890800	Weak transcription	Placenta	Placenta
43	chr2:11888400-11890800	Enhancers	Ovary	ovary
44	chr2:11888400-11891000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:11888400-11891000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:11888400-11891200	Enhancers	Brain Substantia Nigra	brain
47	chr2:11888400-11891400	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr2:11888400-11891400	Enhancers	Left Ventricle	heart
49	chr2:11888400-11891400	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr2:11888400-11891600	Enhancers	Fetal Thymus	thymus

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