Variant report

Variant	rs10939630
Chromosome Location	chr4:15658481-15658482
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:15657650-15658553	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:15655465-15658493	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:15656724-15659017	K562	blood:	n/a	n/a
4	POLR2A	chr4:15658262-15658523	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:15651703..15660794-chr4:15677607..15686235,25	K562	blood:
2	chr4:15654775..15659231-chr4:15659761..15666940,9	K562	blood:
3	chr4:15649873..15653235-chr4:15657425..15660766,3	MCF-7	breast:
4	chr4:15469326..15470996-chr4:15657243..15660173,2	MCF-7	breast:
5	chr4:15656159..15658615-chr4:15712805..15714316,2	K562	blood:
6	chr4:15650206..15660298-chr4:15677140..15687517,25	K562	blood:
7	chr4:15655595..15658742-chr4:15680185..15687360,10	MCF-7	breast:
8	chr4:15652080..15658606-chr4:15677363..15685579,17	MCF-7	breast:

No data

Variant related genes	Relation type
FBXL5	TF binding region
ENSG00000118564	Chromatin interaction
ENSG00000109743	Chromatin interaction
ENSG00000237765	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10011868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516290	1.00[CEU][hapmap]
rs10516291	1.00[CEU][hapmap]
rs1058212	1.00[CEU][hapmap]
rs10939631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11931532	1.00[CEU][hapmap]
rs11934401	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11944132	1.00[CEU][hapmap]
rs12645693	1.00[CEU][hapmap]
rs12646331	1.00[CEU][hapmap]
rs16892141	1.00[CEU][hapmap];0.95[GIH][hapmap]
rs16892263	1.00[CEU][hapmap]
rs16892271	1.00[CEU][hapmap]
rs16892272	1.00[CEU][hapmap]
rs16892276	1.00[CEU][hapmap]
rs16892283	1.00[CEU][hapmap]
rs16892287	1.00[CEU][hapmap]
rs16892289	1.00[CEU][hapmap]
rs16898413	1.00[CEU][hapmap]
rs2302463	1.00[CEU][hapmap]
rs2302464	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes]
rs28392966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4267735	1.00[CEU][hapmap]
rs4321629	1.00[CEU][hapmap]
rs4395498	1.00[CEU][hapmap]
rs4435745	1.00[CEU][hapmap]
rs4498133	1.00[CEU][hapmap]
rs4502676	1.00[CEU][hapmap]
rs6811179	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6828144	1.00[CEU][hapmap]
rs6835705	1.00[CEU][hapmap]
rs6844968	1.00[CEU][hapmap]
rs7657257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7672395	1.00[CEU][hapmap]
rs7683000	0.88[ASN][1000 genomes]
rs7688526	1.00[CEU][hapmap]
rs955410	1.00[CEU][hapmap]
rs9790670	1.00[CEU][hapmap]
rs9942211	1.00[CEU][hapmap]
rs9942247	1.00[CEU][hapmap]
rs9942275	1.00[CEU][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	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	nsv518830	chr4:15610771-15672200	Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	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

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15657200-15662200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr4:15657600-15681400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:15657800-15658800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:15657800-15659000	Weak transcription	Aorta	Aorta
5	chr4:15657800-15659400	Weak transcription	Hela-S3	cervix
6	chr4:15657800-15659400	Weak transcription	HepG2	liver
7	chr4:15657800-15659600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:15657800-15659800	Weak transcription	A549	lung
9	chr4:15657800-15660000	Enhancers	NHDF-Ad	bronchial
10	chr4:15657800-15661400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:15657800-15666800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:15657800-15667800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:15658000-15658600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:15658000-15658800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:15658000-15658800	Weak transcription	Primary T cells from cord blood	blood
16	chr4:15658000-15658800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr4:15658000-15658800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:15658000-15659000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:15658000-15659000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:15658000-15659000	Weak transcription	HSMMtube	muscle
21	chr4:15658000-15659200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:15658000-15659200	Weak transcription	K562	blood
23	chr4:15658000-15659800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:15658000-15660600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr4:15658000-15661400	Weak transcription	Placenta	Placenta
26	chr4:15658000-15664600	Weak transcription	Esophagus	oesophagus
27	chr4:15658000-15665400	Weak transcription	Psoas Muscle	Psoas
28	chr4:15658000-15666800	Weak transcription	Thymus	Thymus
29	chr4:15658000-15667400	Weak transcription	Fetal Muscle Leg	muscle
30	chr4:15658000-15667800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:15658000-15672200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr4:15658000-15673800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:15658000-15675200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:15658000-15679000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr4:15658000-15681400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:15658200-15658600	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr4:15658200-15658600	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr4:15658200-15658600	Weak transcription	HMEC	breast
39	chr4:15658200-15659000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr4:15658200-15659000	Enhancers	Brain Hippocampus Middle	brain
41	chr4:15658200-15659200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:15658200-15659400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr4:15658200-15659400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:15658200-15659400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr4:15658200-15659600	Enhancers	Osteobl	bone
46	chr4:15658200-15659800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr4:15658200-15660200	Enhancers	Fetal Lung	lung
48	chr4:15658200-15660400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:15658200-15661000	Weak transcription	Fetal Heart	heart
50	chr4:15658200-15661200	Weak transcription	Liver	Liver

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