Variant report

Variant	rs4859104
Chromosome Location	chr3:87845957-87845958
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	POLR2A	chr3:87844391-87845969	K562	blood:	n/a	n/a
2	GATA1	chr3:87844998-87846134	K562	blood:	n/a	chr3:87845080-87845090
3	JUND	chr3:87845080-87846092	K562	blood:	n/a	chr3:87845080-87845089 chr3:87845588-87845599
4	CUX1	chr3:87845132-87846197	K562	blood:	n/a	n/a
5	RCOR1	chr3:87845174-87845994	K562	blood:	n/a	n/a
6	JUN	chr3:87845170-87846035	K562	blood:	n/a	n/a
7	IRF1	chr3:87844765-87846951	K562	blood:	n/a	chr3:87845161-87845172 chr3:87846674-87846687
8	GATA1	chr3:87844963-87846100	PBDE	blood:	n/a	chr3:87845080-87845090
9	IRF1	chr3:87844974-87847445	K562	blood:	n/a	chr3:87845161-87845172 chr3:87846674-87846687
10	TBL1XR1	chr3:87844905-87846248	K562	blood:	n/a	n/a
11	IRF1	chr3:87845200-87846194	K562	blood:	n/a	n/a
12	EP300	chr3:87844583-87846481	K562	blood:	n/a	chr3:87844678-87844688 chr3:87845051-87845065 chr3:87845014-87845022
13	EP300	chr3:87845190-87846141	K562	blood:	n/a	n/a
14	SPI1	chr3:87845694-87846003	HL-60	blood:	n/a	n/a
15	ARID3A	chr3:87845165-87845971	K562	blood:	n/a	n/a
16	RCOR1	chr3:87844679-87845979	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:87845525..87848228-chr3:87871993..87873515,2	K562	blood:
2	chr3:87843885..87846211-chr3:87904754..87906414,2	K562	blood:

Variant related genes	Relation type
ENSG00000239572	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12485486	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12488028	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12489435	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1489779	0.92[LWK][hapmap];0.87[YRI][hapmap]
rs1489780	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1873209	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1873210	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046796	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2880695	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4630962	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55754932	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55788242	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55807523	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56125632	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56169023	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56386821	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67303034	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6779623	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7643136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867061	0.81[JPT][hapmap];0.87[TSI][hapmap]

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	nsv590918	chr3:87323334-87910931	Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv877142	chr3:87630433-87854277	Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv877143	chr3:87630433-87860130	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv877144	chr3:87691029-87845957	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv834756	chr3:87763793-87938179	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1009981	chr3:87821573-88003956	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv536634	chr3:87821573-88003956	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4859104	CGGBP1	cis	parietal	SCAN
rs4859104	HTR1F	cis	Thyroid	GTEx
rs4859104	HTR1F	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:87842000-87846200	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr3:87842600-87851000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:87843000-87850400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:87843200-87847200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:87843200-87848200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:87844600-87846000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr3:87844600-87846600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr3:87844600-87847600	Enhancers	Thymus	Thymus
9	chr3:87845200-87846000	Enhancers	Primary T cells from cord blood	blood
10	chr3:87845200-87846000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:87845200-87846200	Enhancers	Primary B cells from cord blood	blood
12	chr3:87845200-87846400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr3:87845400-87846200	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr3:87845600-87847000	Active TSS	K562	blood
15	chr3:87845600-87855800	Weak transcription	A549	lung
16	chr3:87845800-87846200	Active TSS	NHDF-Ad	bronchial

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