Variant report

Variant	rs9661659
Chromosome Location	chr1:224393404-224393405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:224368986..224373517-chr1:224390991..224394171,5	MCF-7	breast:
2	chr1:224374669..224377400-chr1:224391823..224393961,2	K562	blood:
3	chr1:224386204..224388936-chr1:224390782..224393478,2	K562	blood:
4	chr1:224370663..224372600-chr1:224391702..224393896,2	K562	blood:
5	chr1:224392062..224394809-chr1:224425403..224428282,2	K562	blood:
6	chr1:224392534..224394870-chr1:224515641..224518461,2	K562	blood:
7	chr1:224391205..224393756-chr1:224397640..224399675,2	MCF-7	breast:
8	chr1:224387475..224389159-chr1:224391292..224393986,3	MCF-7	breast:
9	chr1:224392784..224394708-chr20:49347702..49350093,2	MCF-7	breast:
10	chr1:224391151..224394255-chr1:224397647..224399379,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000124171	Chromatin interaction
ENSG00000143753	Chromatin interaction
ENSG00000232628	Chromatin interaction
ENSG00000143748	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1060394	0.85[ASN][1000 genomes]
rs10799525	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11589025	0.86[ASN][1000 genomes]
rs12022755	0.86[EUR][1000 genomes];0.88[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	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
3	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv3394698	chr1:224392129-224394152	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
5	esv3339077	chr1:224392629-224393677	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9661659	FBXO28	Cis_1M	lymphoblastoid	RTeQTL
rs9661659	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224389600-224414400	Weak transcription	Fetal Brain Female	brain
2	chr1:224390600-224393800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:224390600-224393800	Enhancers	Fetal Stomach	stomach
4	chr1:224390600-224394400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:224390800-224393600	Enhancers	H1 Cell Line	embryonic stem cell
6	chr1:224390800-224393600	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr1:224390800-224393600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr1:224390800-224393800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:224390800-224393800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:224390800-224393800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr1:224390800-224393800	Enhancers	Placenta	Placenta
12	chr1:224390800-224394000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:224391000-224394000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:224391000-224394600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr1:224391400-224393800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:224391600-224394200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:224391600-224400000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:224391600-224400200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:224391600-224407000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:224391800-224393600	Enhancers	Left Ventricle	heart
21	chr1:224392000-224393600	Enhancers	Lung	lung
22	chr1:224392000-224393600	Flanking Active TSS	Dnd41	blood
23	chr1:224392000-224393800	Enhancers	Primary T cells fromperipheralblood	blood
24	chr1:224392200-224393600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:224392200-224393600	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr1:224392200-224393600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:224392200-224393600	Enhancers	Brain Hippocampus Middle	brain
28	chr1:224392200-224393800	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr1:224392200-224393800	Enhancers	Fetal Thymus	thymus
30	chr1:224392200-224393800	Enhancers	HSMMtube	muscle
31	chr1:224392200-224394400	Enhancers	Fetal Intestine Small	intestine
32	chr1:224392200-224394400	Enhancers	Stomach Mucosa	stomach
33	chr1:224392400-224393600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr1:224392400-224393600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr1:224392400-224393600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:224392400-224393600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:224392400-224393600	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr1:224392400-224393600	Enhancers	Esophagus	oesophagus
39	chr1:224392400-224393600	Enhancers	Ovary	ovary
40	chr1:224392400-224393600	Enhancers	Pancreas	Pancrea
41	chr1:224392400-224393600	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr1:224392400-224393600	Enhancers	Thymus	Thymus
43	chr1:224392400-224393600	Flanking Active TSS	K562	blood
44	chr1:224392400-224393800	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr1:224392400-224393800	Enhancers	Colonic Mucosa	Colon
46	chr1:224392600-224393600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:224392600-224393600	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr1:224392600-224393600	Enhancers	Psoas Muscle	Psoas
49	chr1:224392600-224393600	Enhancers	Right Ventricle	heart
50	chr1:224392600-224393800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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