Variant report

Variant	rs10008878
Chromosome Location	chr4:15674987-15674988
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:15656601..15660282-chr4:15674023..15676952,3	MCF-7	breast:
2	chr4:15480315..15482682-chr4:15674758..15677054,2	MCF-7	breast:
3	chr4:15655677..15658651-chr4:15671837..15675305,4	MCF-7	breast:
4	chr4:15667185..15670762-chr4:15673659..15675755,3	K562	blood:

Variant related genes	Relation type
ENSG00000118564	Chromatin interaction
ENSG00000048342	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10005305	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10015827	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10017222	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10025875	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10034315	0.89[AFR][1000 genomes]
rs10433813	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11722300	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11722854	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11723478	0.95[AFR][1000 genomes]
rs11729955	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11730088	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11732953	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12642407	0.96[AFR][1000 genomes]
rs12650529	0.87[AFR][1000 genomes]
rs13134177	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13150957	0.96[AFR][1000 genomes]
rs17405811	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1786	0.96[AFR][1000 genomes]
rs28394730	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28402170	0.85[AFR][1000 genomes]
rs28447067	0.96[AFR][1000 genomes]
rs28604503	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28644177	0.96[AFR][1000 genomes]
rs28820655	0.94[AFR][1000 genomes]
rs34473224	0.96[AFR][1000 genomes]
rs34559117	0.96[AFR][1000 genomes]
rs35013326	0.94[AFR][1000 genomes]
rs3775956	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3775957	0.96[AFR][1000 genomes]
rs4301111	0.96[AFR][1000 genomes]
rs4331772	0.89[AFR][1000 genomes]
rs4346644	0.96[AFR][1000 genomes]
rs4396986	0.91[AFR][1000 genomes]
rs4423870	0.84[AFR][1000 genomes]
rs4484296	0.94[AFR][1000 genomes]
rs4549375	0.96[AFR][1000 genomes]
rs4554069	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4600905	0.89[AFR][1000 genomes]
rs4698116	0.89[AFR][1000 genomes]
rs6414764	0.96[AFR][1000 genomes]
rs6449152	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6815254	0.87[AFR][1000 genomes]
rs6815296	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6816982	0.94[AFR][1000 genomes]
rs6823775	0.87[AFR][1000 genomes]
rs6824422	0.87[AFR][1000 genomes]
rs6826058	0.96[AFR][1000 genomes]
rs6827406	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6828776	0.86[AFR][1000 genomes]
rs6839654	0.94[AFR][1000 genomes]
rs6843740	0.94[AFR][1000 genomes]
rs6848779	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6852735	0.86[AFR][1000 genomes]
rs6857442	0.93[AFR][1000 genomes]
rs7434484	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7667175	0.94[AFR][1000 genomes]
rs7698596	0.93[AFR][1000 genomes]
rs9994518	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv521183	chr4:15610771-15692136	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv3361772	chr4:15666732-15684418	Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10008878	FBXL5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15657600-15681400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:15658000-15675200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:15658000-15679000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:15658000-15681400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:15658200-15679200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:15658200-15679200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:15658200-15682200	Weak transcription	Fetal Stomach	stomach
8	chr4:15658600-15679000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:15659800-15678600	Weak transcription	K562	blood
10	chr4:15660400-15679200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:15661600-15678600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:15662400-15678800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:15664800-15681800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr4:15667400-15675200	Weak transcription	Fetal Intestine Large	intestine
15	chr4:15668000-15676400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:15668200-15678600	Weak transcription	NHLF	lung
17	chr4:15668400-15679000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr4:15668400-15682800	Weak transcription	Fetal Brain Male	brain
19	chr4:15668600-15677000	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr4:15668600-15678800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:15668600-15679000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr4:15668600-15681400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:15668800-15678600	Weak transcription	Hela-S3	cervix
24	chr4:15669000-15677600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:15669000-15679000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:15669400-15678600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr4:15669400-15678800	Weak transcription	Osteobl	bone
28	chr4:15669600-15679000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr4:15669600-15679000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:15669600-15679000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr4:15669600-15681400	Weak transcription	Thymus	Thymus
32	chr4:15669800-15676600	Weak transcription	GM12878-XiMat	blood
33	chr4:15671000-15678800	Weak transcription	NHDF-Ad	bronchial
34	chr4:15671000-15679000	Weak transcription	HUVEC	blood vessel
35	chr4:15671000-15679200	Weak transcription	Fetal Heart	heart
36	chr4:15671000-15679400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr4:15671000-15681600	Weak transcription	Fetal Lung	lung
38	chr4:15671400-15679000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:15672000-15679000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:15672200-15679000	Weak transcription	HepG2	liver
41	chr4:15672600-15675400	Weak transcription	Primary B cells from cord blood	blood
42	chr4:15672800-15676000	Strong transcription	HSMM	muscle
43	chr4:15672800-15676200	Weak transcription	Primary B cells from peripheral blood	blood
44	chr4:15673000-15675000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr4:15673000-15675600	Strong transcription	Dnd41	blood
46	chr4:15673200-15680800	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr4:15673400-15675600	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr4:15673800-15675400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:15673800-15675600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:15673800-15678600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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