Variant report

Variant	rs2762112
Chromosome Location	chr13:94050688-94050689
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	CEBPB	chr13:94050505-94050875	IMR90	lung:	n/a	chr13:94050685-94050696 chr13:94050687-94050696 chr13:94050687-94050696 chr13:94050687-94050696 chr13:94050687-94050696 chr13:94050685-94050698 chr13:94050685-94050698 chr13:94050686-94050697
2	CEBPB	chr13:94050523-94050763	HepG2	liver:	n/a	chr13:94050685-94050696 chr13:94050687-94050696 chr13:94050687-94050696 chr13:94050687-94050696 chr13:94050687-94050696 chr13:94050685-94050698 chr13:94050685-94050698 chr13:94050686-94050697

Variant related genes	Relation type
HNRNPA1P29	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10508000	0.81[EUR][1000 genomes]
rs10508001	0.81[EUR][1000 genomes]
rs10508002	0.81[EUR][1000 genomes]
rs10508003	0.81[EUR][1000 genomes]
rs10508004	0.80[EUR][1000 genomes]
rs10508005	0.80[EUR][1000 genomes]
rs10851334	0.81[EUR][1000 genomes]
rs11619994	0.80[EUR][1000 genomes]
rs11838734	0.80[EUR][1000 genomes]
rs11841335	0.80[EUR][1000 genomes]
rs11843793	0.80[EUR][1000 genomes]
rs12854387	0.81[EUR][1000 genomes]
rs12855239	0.81[EUR][1000 genomes]
rs12855671	0.80[EUR][1000 genomes]
rs12860734	0.80[EUR][1000 genomes]
rs12866595	0.80[EUR][1000 genomes]
rs12874982	0.81[EUR][1000 genomes]
rs12875395	0.84[EUR][1000 genomes]
rs12876057	0.80[EUR][1000 genomes]
rs12877660	0.80[EUR][1000 genomes]
rs16948775	0.81[EUR][1000 genomes]
rs16948800	0.80[EUR][1000 genomes]
rs16948803	0.80[EUR][1000 genomes]
rs16952683	0.81[EUR][1000 genomes]
rs17188977	0.81[EUR][1000 genomes]
rs17267683	0.91[EUR][1000 genomes]
rs17267711	0.81[EUR][1000 genomes]
rs17267738	0.80[EUR][1000 genomes]
rs17267745	0.80[EUR][1000 genomes]
rs1886205	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2762088	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2762091	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2762098	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2762108	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2762111	0.82[AFR][1000 genomes]
rs2762115	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2892657	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34119608	0.81[EUR][1000 genomes]
rs34136695	0.80[EUR][1000 genomes]
rs4644730	0.82[EUR][1000 genomes]
rs56228951	0.80[EUR][1000 genomes]
rs61964173	0.81[EUR][1000 genomes]
rs61964175	0.80[EUR][1000 genomes]
rs7317246	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7325511	0.80[EUR][1000 genomes]
rs7325937	0.80[EUR][1000 genomes]
rs7329962	0.81[EUR][1000 genomes]
rs7331613	0.80[EUR][1000 genomes]
rs7338634	0.80[EUR][1000 genomes]
rs73552665	0.80[EUR][1000 genomes]
rs74108531	0.80[EUR][1000 genomes]
rs7994743	0.80[EUR][1000 genomes]
rs7998675	0.80[EUR][1000 genomes]
rs7998856	0.80[EUR][1000 genomes]
rs7999019	0.80[EUR][1000 genomes]
rs7999482	0.80[EUR][1000 genomes]
rs8000632	0.80[EUR][1000 genomes]
rs8000987	0.80[EUR][1000 genomes]
rs920954	0.80[EUR][1000 genomes]
rs920955	0.80[EUR][1000 genomes]
rs9524047	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869070	chr13:93347616-94286933	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1053035	chr13:93842576-94229732	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv541880	chr13:93842576-94229732	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv530636	chr13:93997311-94281707	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv916039	chr13:94035909-94191105	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2762112	GPC6	cis	Thyroid	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94046600-94052400	Weak transcription	Fetal Brain Male	brain
2	chr13:94047800-94057200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr13:94049600-94051400	Enhancers	Osteobl	bone
4	chr13:94049800-94050800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr13:94050000-94050800	Enhancers	Fetal Stomach	stomach
6	chr13:94050000-94051000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr13:94050200-94050800	Enhancers	Colon Smooth Muscle	Colon
8	chr13:94050200-94050800	Enhancers	HSMM	muscle
9	chr13:94050200-94051000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr13:94050200-94051000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr13:94050200-94051000	Enhancers	Fetal Heart	heart
12	chr13:94050200-94051800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr13:94050600-94050800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr13:94050600-94050800	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr13:94050600-94051400	Enhancers	Adipose Nuclei	Adipose
16	chr13:94050600-94051600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr13:94050600-94052000	Enhancers	A549	lung

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