Variant report

Variant	rs10516459
Chromosome Location	chr4:100848952-100848953
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	CEBPB	chr4:100848826-100849015	HepG2	liver:	n/a	n/a
2	STAT3	chr4:100848793-100848974	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:100840471..100849591-chr4:100866268..100873122,18	K562	blood:
2	chr4:100815570..100818331-chr4:100848090..100849658,2	K562	blood:
3	chr4:100848205..100853069-chr4:100866591..100869335,5	MCF-7	breast:

Variant related genes	Relation type
DNAJB14	TF binding region
ENSG00000109270	Chromatin interaction
ENSG00000164032	Chromatin interaction
ENSG00000164031	Chromatin interaction
ENSG00000245322	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11554389	1.00[LWK][hapmap]
rs12431	0.95[EUR][1000 genomes]
rs15788	1.00[LWK][hapmap]
rs15924	1.00[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes]
rs17539582	0.89[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs17539883	0.95[EUR][1000 genomes]
rs17541426	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17541690	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17612178	0.83[EUR][1000 genomes]
rs17613746	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17614270	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2866181	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs41275723	0.97[EUR][1000 genomes]
rs62305039	0.83[EUR][1000 genomes]
rs62305041	0.93[EUR][1000 genomes]
rs62305044	0.83[EUR][1000 genomes]
rs62305046	0.97[EUR][1000 genomes]
rs62305049	0.85[EUR][1000 genomes]
rs62305052	0.97[EUR][1000 genomes]
rs62305053	0.97[EUR][1000 genomes]
rs62305055	0.97[EUR][1000 genomes]
rs62305056	0.98[EUR][1000 genomes]
rs62305057	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62305059	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62306060	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62306061	0.87[EUR][1000 genomes]
rs62306063	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62306064	0.83[EUR][1000 genomes]
rs62306066	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62306067	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62306068	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62306069	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62306070	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62306071	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62306072	0.80[EUR][1000 genomes]
rs62306073	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62306075	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62306084	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62306085	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62306111	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62306113	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62306115	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62306136	0.85[AMR][1000 genomes]
rs767652	0.89[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879661	chr4:100805207-100869635	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10516459	CBR3	trans	lymphoblastoid	seeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100816000-100867000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:100816000-100867000	Weak transcription	Lung	lung
3	chr4:100816200-100851400	Weak transcription	A549	lung
4	chr4:100816200-100851600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:100816200-100853600	Weak transcription	NHLF	lung
6	chr4:100816200-100866200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:100820000-100866200	Weak transcription	Fetal Heart	heart
8	chr4:100824000-100865800	Weak transcription	Psoas Muscle	Psoas
9	chr4:100824400-100866000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:100824800-100854200	Weak transcription	Brain Anterior Caudate	brain
11	chr4:100827600-100856400	Weak transcription	Brain Substantia Nigra	brain
12	chr4:100828800-100866200	Weak transcription	Stomach Mucosa	stomach
13	chr4:100829200-100856400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:100829200-100866600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:100829400-100852600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr4:100829400-100856200	Weak transcription	HepG2	liver
17	chr4:100829600-100866200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr4:100836600-100856800	Weak transcription	Spleen	Spleen
19	chr4:100836800-100851800	Strong transcription	Dnd41	blood
20	chr4:100837600-100852600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr4:100838200-100850200	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr4:100838400-100850000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:100838400-100852000	Strong transcription	Fetal Thymus	thymus
24	chr4:100839000-100852200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:100839200-100855600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:100839200-100857400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:100840000-100852800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr4:100840000-100862600	Weak transcription	K562	blood
29	chr4:100840200-100854000	Weak transcription	Brain Germinal Matrix	brain
30	chr4:100840200-100864600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr4:100840200-100865800	Weak transcription	Ovary	ovary
32	chr4:100840200-100866000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr4:100840200-100867000	Weak transcription	Gastric	stomach
34	chr4:100840400-100850000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:100840400-100850400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:100840400-100851000	Weak transcription	Fetal Brain Male	brain
37	chr4:100840400-100851400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr4:100840400-100851600	Weak transcription	Fetal Brain Female	brain
39	chr4:100840400-100852400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr4:100840400-100855000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:100840400-100855200	Weak transcription	Colon Smooth Muscle	Colon
42	chr4:100840400-100856400	Weak transcription	Fetal Kidney	kidney
43	chr4:100840400-100856400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr4:100840400-100856800	Weak transcription	Thymus	Thymus
45	chr4:100840400-100864600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr4:100840400-100866800	Weak transcription	Aorta	Aorta
47	chr4:100840400-100867000	Weak transcription	Esophagus	oesophagus
48	chr4:100840600-100850200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr4:100840600-100852000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr4:100840600-100862200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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