Variant report

Variant	rs5020877
Chromosome Location	chr2:11694370-11694371
allele	A/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	MAX	chr2:11694288-11694813	NB4	blood:	n/a	n/a
2	POLR2A	chr2:11693148-11694987	MCF-7	breast:	n/a	n/a
3	POLR2A	chr2:11694124-11694938	HepG2	liver:	n/a	n/a
4	KAP1	chr2:11694217-11694473	U2OS	brain:	n/a	n/a
5	SPI1	chr2:11694268-11694763	HL-60	blood:	n/a	n/a
6	REST	chr2:11694249-11694638	PFSK-1	brain:	n/a	chr2:11694393-11694406
7	MYC	chr2:11694250-11694775	NB4	blood:	n/a	n/a
8	REST	chr2:11694174-11694480	PFSK-1	brain:	n/a	chr2:11694393-11694406

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11693244..11695539-chr2:11699023..11701494,2	K562	blood:
2	chr2:11694156..11696211-chr2:11713975..11716085,2	K562	blood:

Variant related genes	Relation type
GREB1	TF binding region
ENSG00000251718	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10427206	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10495583	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4313952	0.90[CEU][hapmap]
rs58738000	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61039324	0.87[ASN][1000 genomes]
rs6432210	0.88[CEU][hapmap]
rs6432211	0.90[CEU][hapmap]
rs6432212	0.88[CEU][hapmap]
rs6432213	0.90[CEU][hapmap]
rs6432214	0.90[CEU][hapmap]
rs6432215	0.88[CEU][hapmap]
rs6432216	0.88[CEU][hapmap]
rs6710534	0.82[EUR][1000 genomes]
rs6718650	0.89[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6728463	0.82[EUR][1000 genomes]
rs6745409	0.89[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6749404	0.90[CEU][hapmap]
rs68152859	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72772060	0.87[ASN][1000 genomes]
rs73915431	0.87[ASN][1000 genomes]
rs73915432	0.83[ASN][1000 genomes]
rs7564191	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs930310	0.88[CEU][hapmap]
rs9784026	0.87[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9784028	0.89[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv873663	chr2:11664349-11783775	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv1814335	chr2:11689048-11718858	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11678400-11757000	Weak transcription	Right Ventricle	heart
2	chr2:11683400-11697800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr2:11687000-11694600	Weak transcription	Brain Substantia Nigra	brain
4	chr2:11688600-11696400	Weak transcription	Pancreas	Pancrea
5	chr2:11690000-11711000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:11691000-11694800	Genic enhancers	HepG2	liver
7	chr2:11691000-11697600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:11691400-11696200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:11691400-11697600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:11691400-11699800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:11693200-11695000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:11693600-11694800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
13	chr2:11693800-11694400	Enhancers	Adipose Nuclei	Adipose
14	chr2:11693800-11694400	Enhancers	Placenta	Placenta
15	chr2:11693800-11694600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:11693800-11694800	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr2:11693800-11694800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:11693800-11694800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:11693800-11694800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:11693800-11694800	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr2:11694000-11694400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
22	chr2:11694000-11694600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr2:11694000-11694800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:11694000-11694800	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr2:11694000-11694800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr2:11694000-11694800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:11694000-11694800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:11694000-11694800	Transcr. at gene 5' and 3'	Ovary	ovary
29	chr2:11694000-11694800	Bivalent Enhancer	HSMMtube	muscle
30	chr2:11694000-11694800	Bivalent Enhancer	Osteobl	bone
31	chr2:11694000-11695000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:11694200-11694400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
33	chr2:11694200-11694400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
34	chr2:11694200-11694600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:11694200-11694800	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr2:11694200-11694800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:11694200-11694800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:11694200-11694800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:11694200-11694800	Enhancers	Fetal Lung	lung
40	chr2:11694200-11694800	Enhancers	Gastric	stomach
41	chr2:11694200-11694800	Enhancers	GM12878-XiMat	blood
42	chr2:11694200-11694800	Bivalent Enhancer	HMEC	breast
43	chr2:11694200-11695800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:11694200-11698400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr2:11694200-11698400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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