Variant report

Variant	rs28644177
Chromosome Location	chr4:15658735-15658736
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:15656724-15659017	K562	blood:	n/a	n/a

No data

(count:6 , 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	chr4:15650206..15660298-chr4:15677140..15687517,25	K562	blood:
6	chr4:15655595..15658742-chr4:15680185..15687360,10	MCF-7	breast:

No data

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

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10005305	0.94[AFR][1000 genomes]
rs10008878	0.96[AFR][1000 genomes]
rs10009089	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10025875	0.96[AFR][1000 genomes]
rs10034315	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11722757	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11722854	0.81[ASN][1000 genomes]
rs11723478	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11726647	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11732953	0.92[AFR][1000 genomes]
rs12642407	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650529	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13134177	0.91[AFR][1000 genomes]
rs13150957	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28394730	0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs28402170	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28447067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28604503	0.81[ASN][1000 genomes]
rs28820655	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34473224	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34559117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34955342	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35013326	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35120298	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3756247	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3775956	0.97[AFR][1000 genomes]
rs3775957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4257653	0.98[ASN][1000 genomes]
rs4301111	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4331772	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4346644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4396986	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4423870	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4484296	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4549375	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4554069	0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4600905	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698116	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6414764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6449150	0.81[AFR][1000 genomes]
rs6815254	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6816982	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6823775	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6824422	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6825051	0.83[AFR][1000 genomes]
rs6826058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6828776	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6839654	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6843740	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6848779	0.96[AFR][1000 genomes]
rs6852735	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6857442	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7434484	0.81[ASN][1000 genomes]
rs7667175	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7698596	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9994518	0.97[AFR][1000 genomes];0.81[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	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:80 , 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	chr4:15658000-15658800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:15658000-15658800	Weak transcription	Primary T cells from cord blood	blood
15	chr4:15658000-15658800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr4:15658000-15658800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:15658000-15659000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:15658000-15659000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:15658000-15659000	Weak transcription	HSMMtube	muscle
20	chr4:15658000-15659200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:15658000-15659200	Weak transcription	K562	blood
22	chr4:15658000-15659800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:15658000-15660600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
24	chr4:15658000-15661400	Weak transcription	Placenta	Placenta
25	chr4:15658000-15664600	Weak transcription	Esophagus	oesophagus
26	chr4:15658000-15665400	Weak transcription	Psoas Muscle	Psoas
27	chr4:15658000-15666800	Weak transcription	Thymus	Thymus
28	chr4:15658000-15667400	Weak transcription	Fetal Muscle Leg	muscle
29	chr4:15658000-15667800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:15658000-15672200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr4:15658000-15673800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:15658000-15675200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:15658000-15679000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr4:15658000-15681400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:15658200-15659000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr4:15658200-15659000	Enhancers	Brain Hippocampus Middle	brain
37	chr4:15658200-15659200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:15658200-15659400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:15658200-15659400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:15658200-15659400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr4:15658200-15659600	Enhancers	Osteobl	bone
42	chr4:15658200-15659800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr4:15658200-15660200	Enhancers	Fetal Lung	lung
44	chr4:15658200-15660400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:15658200-15661000	Weak transcription	Fetal Heart	heart
46	chr4:15658200-15661200	Weak transcription	Liver	Liver
47	chr4:15658200-15661600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:15658200-15661800	Active TSS	Primary B cells from cord blood	blood
49	chr4:15658200-15665000	Weak transcription	GM12878-XiMat	blood
50	chr4:15658200-15666600	Weak transcription	HUVEC	blood vessel

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