Variant report

Variant	rs12491236
Chromosome Location	chr3:46688481-46688482
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	FOS	chr3:46688234-46688539	MCF10A-Er-Src	breast:	n/a	chr3:46688385-46688395 chr3:46688386-46688394 chr3:46688384-46688395 chr3:46688385-46688395
2	MAX	chr3:46688272-46688660	SK-N-SH	brain:	n/a	n/a
3	MAX	chr3:46688214-46688636	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr3:46688037-46688611	SK-N-SH	brain:	n/a	n/a
5	FOS	chr3:46688307-46688507	MCF10A-Er-Src	breast:	n/a	chr3:46688385-46688395 chr3:46688386-46688394 chr3:46688384-46688395 chr3:46688385-46688395
6	TCF12	chr3:46688137-46688764	SK-N-SH	brain:	n/a	n/a
7	MYC	chr3:46688255-46688558	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr3:46688254-46688507	MCF10A-Er-Src	breast:	n/a	chr3:46688385-46688395 chr3:46688386-46688394 chr3:46688384-46688395 chr3:46688385-46688395
9	FOS	chr3:46688233-46688519	MCF10A-Er-Src	breast:	n/a	chr3:46688385-46688395 chr3:46688386-46688394 chr3:46688384-46688395 chr3:46688385-46688395
10	STAT3	chr3:46688305-46688596	MCF10A-Er-Src	breast:	n/a	n/a
11	MYC	chr3:46688263-46688542	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000251967	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11130099	0.92[ASN][1000 genomes]
rs11130102	0.82[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11710586	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11719679	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11922418	0.93[ASN][1000 genomes]
rs12491294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13083665	0.93[ASN][1000 genomes]
rs1402148	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1520488	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1520489	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1581325	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1607737	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34000414	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34063921	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34820891	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4234464	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4683256	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683260	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs4683271	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59048074	0.83[ASN][1000 genomes]
rs6442011	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6442012	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6773430	0.81[JPT][hapmap]
rs6774048	0.82[CEU][hapmap]
rs6808214	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7373994	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs7643859	0.85[ASN][1000 genomes]
rs7644072	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs877680	0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs877681	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs950190	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9845998	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv876739	chr3:46656980-46744966	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv876740	chr3:46656980-46748453	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv876741	chr3:46663372-46763839	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv516623	chr3:46680063-46852679	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12491236	ALS2CL	cis	cerebellum	SCAN
rs12491236	LRRC2	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46687800-46688800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:46687800-46688800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr3:46687800-46688800	Enhancers	NHLF	lung
4	chr3:46687800-46689200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:46687800-46689200	Enhancers	NHDF-Ad	bronchial
6	chr3:46688000-46688800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:46688000-46688800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:46688000-46688800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:46688000-46688800	Enhancers	Left Ventricle	heart
10	chr3:46688000-46688800	Enhancers	HMEC	breast
11	chr3:46688200-46688600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:46688200-46688600	Enhancers	HSMM	muscle
13	chr3:46688200-46688800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:46688400-46688600	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr3:46688400-46688600	Enhancers	NHEK	skin
16	chr3:46688400-46700800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links