Variant report

Variant	rs13097697
Chromosome Location	chr3:19986489-19986490
allele	C/T
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	CEBPB	chr3:19986340-19986696	K562	blood:	n/a	n/a
2	CEBPB	chr3:19986412-19986685	IMR90	lung:	n/a	n/a
3	POLR2A	chr3:19986265-20000717	K562	blood:	n/a	n/a
4	JUN	chr3:19986345-19989634	K562	blood:	n/a	chr3:19989188-19989197 chr3:19989189-19989198 chr3:19989190-19989201 chr3:19989187-19989199 chr3:19989188-19989198
5	CEBPB	chr3:19986152-19986668	A549	lung:	n/a	chr3:19986227-19986240

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:19985145..19990136-chr3:20225418..20228312,6	K562	blood:
2	chr3:19971930..19974485-chr3:19985453..19987123,2	MCF-7	breast:

Variant related genes	Relation type
RAB5A	TF binding region
HSPA8P18	TF binding region
ENSG00000129810	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11128928	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11128929	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11128930	0.95[EUR][1000 genomes]
rs11128931	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1133328	1.00[ASN][1000 genomes]
rs1143451	0.95[EUR][1000 genomes]
rs12629485	0.94[EUR][1000 genomes]
rs13065319	0.92[EUR][1000 genomes]
rs13070718	0.81[EUR][1000 genomes]
rs13076973	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13078505	0.93[EUR][1000 genomes]
rs13082980	0.88[EUR][1000 genomes]
rs13086159	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13089853	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13098388	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17181400	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17181862	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs17796115	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34305656	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34343204	0.95[EUR][1000 genomes]
rs34417128	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs34705953	0.87[AFR][1000 genomes]
rs35175665	0.95[EUR][1000 genomes]
rs35713165	0.97[EUR][1000 genomes]
rs4610240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59608170	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60255931	0.88[EUR][1000 genomes]
rs62241278	0.93[ASN][1000 genomes]
rs6796425	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs71316239	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7434271	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615145	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7618928	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7634934	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7646128	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9877801	0.88[EUR][1000 genomes]
rs9878879	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs13097697	EFHB,LOC100130288	cis	occipital cortex	BrainEAC
rs13097697	EFHB	cis	Thyroid	GTEx
rs13097697	EFHB,LOC100130288	cis	temporal cortex	BrainEAC
rs13097697	EFHB,LOC100130288	cis	brain	BrainEAC
rs13097697	EFHB,LOC100130288	cis	hippocampus	BrainEAC
rs13097697	EFHB,LOC100130288	cis	cerebellar cortex	BrainEAC
rs13097697	EFHB	cis	Muscle Skeletal	GTEx
rs13097697	EFHB,LOC100130288	cis	frontal cortex	BrainEAC
rs13097697	EFHB	cis	Artery Tibial	GTEx
rs13097697	EFHB	cis	Skin Sun Exposed Lower leg	GTEx
rs13097697	EFHB	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19973600-19987200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr3:19975600-19987400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:19976000-19987400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:19979600-19987600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:19979600-19987800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:19980000-19986600	Weak transcription	K562	blood
7	chr3:19982200-19987200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:19983200-19987400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:19983800-19987600	Weak transcription	Aorta	Aorta
10	chr3:19984600-19987400	Weak transcription	Brain Germinal Matrix	brain
11	chr3:19984800-19987200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:19984800-19987200	Weak transcription	Adipose Nuclei	Adipose
13	chr3:19984800-19987600	Weak transcription	Esophagus	oesophagus
14	chr3:19985000-19987000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:19985000-19987400	Weak transcription	HSMM	muscle
16	chr3:19985600-19987600	Weak transcription	Fetal Lung	lung
17	chr3:19985800-19987400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:19985800-19987400	Weak transcription	NH-A	brain
19	chr3:19986200-19986800	Enhancers	A549	lung
20	chr3:19986400-19987000	Weak transcription	Muscle Satellite Cultured Cells	--

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