Variant report

Variant	rs1789
Chromosome Location	chr4:15664535-15664536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:15664452-15666087	K562	blood:	n/a	n/a
2	FOXA1	chr4:15664401-15664754	HepG2	liver:	n/a	chr4:15664608-15664623 chr4:15664578-15664593

No.	Distal block	Cell Line	Cell type
1	chr4:15664444..15667043-chr4:15668246..15669921,2	K562	blood:
2	chr4:15663938..15667635-chr4:15670287..15673065,4	K562	blood:
3	chr4:15662285..15665284-chr4:15678264..15680948,2	MCF-7	breast:
4	chr4:15659405..15662406-chr4:15663977..15668803,5	MCF-7	breast:
5	chr4:15654775..15659231-chr4:15659761..15666940,9	K562	blood:

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

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10008376	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10008975	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10214	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11728084	0.86[EUR][1000 genomes]
rs12499412	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12500587	0.86[EUR][1000 genomes]
rs12500770	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12512883	0.83[EUR][1000 genomes]
rs12644655	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12651550	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13110674	0.89[EUR][1000 genomes]
rs13120905	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13129739	0.82[EUR][1000 genomes]
rs13147590	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35414597	0.83[EUR][1000 genomes]
rs4235379	0.90[EUR][1000 genomes]
rs4270584	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4333182	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4453929	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4470622	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4524378	0.88[EUR][1000 genomes]
rs4557256	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4616746	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4631041	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4698402	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4698404	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698406	0.90[EUR][1000 genomes]
rs4698407	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698409	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61021642	0.86[EUR][1000 genomes]
rs6414765	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6414767	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6414768	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6449153	0.93[EUR][1000 genomes]
rs6449161	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6850169	0.86[EUR][1000 genomes]
rs6850422	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7438356	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7662032	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7685083	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7687003	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7688984	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7696127	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8180240	0.80[AFR][1000 genomes]
rs9997068	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.98[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1789	FBXL5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 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	chr4:15657800-15666800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:15657800-15667800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:15658000-15664600	Weak transcription	Esophagus	oesophagus
5	chr4:15658000-15665400	Weak transcription	Psoas Muscle	Psoas
6	chr4:15658000-15666800	Weak transcription	Thymus	Thymus
7	chr4:15658000-15667400	Weak transcription	Fetal Muscle Leg	muscle
8	chr4:15658000-15667800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:15658000-15672200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr4:15658000-15673800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:15658000-15675200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:15658000-15679000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:15658000-15681400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:15658200-15665000	Weak transcription	GM12878-XiMat	blood
15	chr4:15658200-15666600	Weak transcription	HUVEC	blood vessel
16	chr4:15658200-15666800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr4:15658200-15667200	Weak transcription	Fetal Thymus	thymus
18	chr4:15658200-15667400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:15658200-15667400	Weak transcription	NH-A	brain
20	chr4:15658200-15667800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr4:15658200-15667800	Weak transcription	NHLF	lung
22	chr4:15658200-15668000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr4:15658200-15670600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr4:15658200-15679200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:15658200-15679200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr4:15658200-15682200	Weak transcription	Fetal Stomach	stomach
27	chr4:15658400-15667000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr4:15658400-15667400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:15658400-15668400	Weak transcription	Dnd41	blood
30	chr4:15658400-15668600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr4:15658600-15673000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:15658600-15679000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr4:15659600-15668200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr4:15659800-15678600	Weak transcription	K562	blood
35	chr4:15660000-15667400	Weak transcription	HSMMtube	muscle
36	chr4:15660000-15667400	Weak transcription	NHDF-Ad	bronchial
37	chr4:15660000-15668600	Weak transcription	HepG2	liver
38	chr4:15660200-15665800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:15660200-15670600	Weak transcription	Fetal Lung	lung
40	chr4:15660400-15679200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr4:15661200-15668000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:15661400-15667400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:15661600-15667200	Weak transcription	A549	lung
44	chr4:15661600-15667600	Weak transcription	Osteobl	bone
45	chr4:15661600-15668400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:15661600-15668800	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr4:15661600-15678600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:15661800-15665200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr4:15661800-15667200	Weak transcription	HSMM	muscle
50	chr4:15662000-15667000	Weak transcription	Adipose Nuclei	Adipose

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