Variant report

Variant	rs10915942
Chromosome Location	chr1:226305741-226305742
allele	A/G
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226247784..226253760-chr1:226305545..226317702,29	MCF-7	breast:
2	chr1:226176946..226178537-chr1:226305551..226307397,2	K562	blood:
3	chr1:226295177..226301855-chr1:226303668..226313005,25	K562	blood:
4	chr1:226299228..226300786-chr1:226305720..226307494,2	K562	blood:
5	chr1:226304646..226307076-chr1:226314160..226316029,2	K562	blood:
6	chr1:226245827..226258736-chr1:226304107..226314743,27	K562	blood:
7	chr1:226292376..226295257-chr1:226305072..226307730,3	MCF-7	breast:
8	chr1:226303513..226307082-chr1:226307356..226312783,6	K562	blood:
9	chr1:226295676..226301816-chr1:226302378..226313716,36	MCF-7	breast:
10	chr1:226245827..226262488-chr1:226303989..226311845,34	K562	blood:
11	chr1:226305715..226313141-chr1:226367413..226376964,17	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272562	Chromatin interaction
ENSG00000270598	Chromatin interaction
ENSG00000223570	Chromatin interaction
ENSG00000163041	Chromatin interaction
ENSG00000182827	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10753414	0.88[EUR][1000 genomes]
rs11589277	0.87[EUR][1000 genomes]
rs12081020	0.86[EUR][1000 genomes]
rs1219670	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1219672	0.88[EUR][1000 genomes]
rs16860148	0.82[JPT][hapmap]
rs1877159	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4278344	0.80[AMR][1000 genomes];0.94[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	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	esv1792510	chr1:226277560-226323824	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10915942	FBXO28	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226299000-226308800	Weak transcription	A549	lung
2	chr1:226299600-226308400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:226299600-226308800	Weak transcription	Fetal Intestine Small	intestine
4	chr1:226299800-226306800	Weak transcription	Spleen	Spleen
5	chr1:226299800-226308800	Weak transcription	Gastric	stomach
6	chr1:226299800-226309000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:226300000-226308200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:226300000-226308200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:226300400-226306000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:226301000-226306000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:226301000-226306600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:226301400-226306200	Weak transcription	Primary B cells from cord blood	blood
13	chr1:226301800-226306000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr1:226304000-226306400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:226304000-226307400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:226304000-226308000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:226304000-226308000	Weak transcription	Fetal Thymus	thymus
18	chr1:226304000-226308800	Weak transcription	HMEC	breast
19	chr1:226304000-226308800	Weak transcription	NHEK	skin
20	chr1:226304200-226308800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:226304200-226308800	Weak transcription	Esophagus	oesophagus
22	chr1:226304600-226308800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:226305000-226306000	Weak transcription	K562	blood
24	chr1:226305600-226305800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:226305600-226306200	Enhancers	HSMMtube	muscle
26	chr1:226305600-226306600	Enhancers	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links