Variant report

Variant	rs900826
Chromosome Location	chr15:59681214-59681215
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	FOSL2	chr15:59680783-59681263	SK-N-SH	brain:	n/a	chr15:59681015-59681022 chr15:59681015-59681024 chr15:59681014-59681023 chr15:59681015-59681023 chr15:59681014-59681024
2	FOS	chr15:59680822-59681241	MCF10A-Er-Src	breast:	n/a	chr15:59681015-59681022 chr15:59681015-59681024 chr15:59681014-59681023 chr15:59681015-59681023 chr15:59681013-59681024 chr15:59681014-59681024
3	CEBPB	chr15:59680609-59681403	A549	lung:	n/a	chr15:59680978-59680989
4	CEBPB	chr15:59680732-59681305	A549	lung:	n/a	chr15:59680978-59680989
5	CEBPB	chr15:59680694-59681297	HCT-116	colon:	n/a	chr15:59680978-59680989
6	CEBPB	chr15:59680755-59681245	HCT-116	colon:	n/a	chr15:59680978-59680989
7	JUND	chr15:59680750-59681268	SK-N-SH	brain:	n/a	chr15:59681015-59681022 chr15:59681015-59681024 chr15:59681014-59681023 chr15:59681013-59681024 chr15:59681015-59681023 chr15:59681014-59681024
8	JUND	chr15:59680755-59681264	Hela-S3	cervix:	n/a	chr15:59681015-59681022 chr15:59681015-59681024 chr15:59681014-59681023 chr15:59681013-59681024 chr15:59681015-59681023 chr15:59681014-59681024
9	STAT3	chr15:59681042-59681226	MCF10A-Er-Src	breast:	n/a	n/a
10	JUN	chr15:59680812-59681227	Hela-S3	cervix:	n/a	chr15:59681015-59681022 chr15:59681015-59681024 chr15:59681014-59681023 chr15:59681015-59681023 chr15:59681014-59681024
11	FOS	chr15:59680805-59681216	MCF10A-Er-Src	breast:	n/a	chr15:59681015-59681022 chr15:59681015-59681024 chr15:59681014-59681023 chr15:59681015-59681023 chr15:59681013-59681024 chr15:59681014-59681024
12	FOS	chr15:59680825-59681221	Hela-S3	cervix:	n/a	chr15:59681015-59681022 chr15:59681015-59681024 chr15:59681014-59681023 chr15:59681015-59681023 chr15:59681013-59681024 chr15:59681014-59681024
13	JUND	chr15:59680847-59681244	A549	lung:	n/a	chr15:59681015-59681022 chr15:59681015-59681024 chr15:59681014-59681023 chr15:59681013-59681024 chr15:59681015-59681023 chr15:59681014-59681024
14	FOSL2	chr15:59680700-59681401	A549	lung:	n/a	chr15:59681015-59681022 chr15:59681015-59681024 chr15:59681014-59681023 chr15:59681015-59681023 chr15:59681014-59681024
15	FOSL1	chr15:59680757-59681369	HCT-116	colon:	n/a	chr15:59681015-59681022 chr15:59681015-59681024 chr15:59681014-59681023 chr15:59681015-59681023 chr15:59681014-59681024
16	CEBPB	chr15:59680762-59681241	Hela-S3	cervix:	n/a	chr15:59680978-59680989
17	FOS	chr15:59680824-59681225	MCF10A-Er-Src	breast:	n/a	chr15:59681015-59681022 chr15:59681015-59681024 chr15:59681014-59681023 chr15:59681015-59681023 chr15:59681013-59681024 chr15:59681014-59681024
18	JUND	chr15:59680615-59681361	SK-N-SH	brain:	n/a	chr15:59681015-59681022 chr15:59681015-59681024 chr15:59681014-59681023 chr15:59681013-59681024 chr15:59681015-59681023 chr15:59681014-59681024

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59680945..59682711-chr15:59948219..59950781,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238767	TF binding region
ENSG00000140307	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11071434	0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs11071435	0.83[YRI][hapmap]
rs11071436	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11631332	0.87[EUR][1000 genomes]
rs11854940	0.82[AFR][1000 genomes]
rs11855994	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12101897	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12439872	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439881	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439906	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439956	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591636	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12593938	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28549269	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61654958	0.87[EUR][1000 genomes]
rs66788165	0.87[EUR][1000 genomes]
rs71480523	0.85[AFR][1000 genomes]
rs7164525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727634	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727635	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023491	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs900825	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs900828	0.89[LWK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv934082	chr15:59608605-59733211	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv457175	chr15:59609753-59681214	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv569603	chr15:59609753-59681214	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv471246	chr15:59610743-59681214	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv904274	chr15:59623576-59689378	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv904275	chr15:59648633-59726610	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	n/a
8	nsv904276	chr15:59648633-59743010	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	n/a
9	nsv904277	chr15:59666992-59705005	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
10	nsv524569	chr15:59666992-59712427	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
11	nsv984078	chr15:59673640-59683792	Weak transcription Enhancers Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs900826	CCDC112	trans	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59665800-59691800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:59666200-59681800	Weak transcription	Ovary	ovary
3	chr15:59667400-59691800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:59670400-59685000	Weak transcription	Primary B cells from cord blood	blood
5	chr15:59673600-59685200	Weak transcription	Fetal Intestine Small	intestine
6	chr15:59674400-59682200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr15:59675200-59688200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:59675200-59703000	Weak transcription	Aorta	Aorta
9	chr15:59677600-59686200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:59678000-59693400	Weak transcription	Liver	Liver
11	chr15:59679800-59686000	Weak transcription	Placenta	Placenta
12	chr15:59680200-59681400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:59680200-59685600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr15:59680600-59681400	Enhancers	A549	lung
15	chr15:59680800-59681400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:59680800-59681400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr15:59680800-59681400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr15:59680800-59681400	Enhancers	NHLF	lung
19	chr15:59680800-59681400	Enhancers	Osteobl	bone
20	chr15:59681000-59681400	Flanking Active TSS	Hela-S3	cervix
21	chr15:59681000-59685200	Weak transcription	GM12878-XiMat	blood
22	chr15:59681200-59681400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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