Variant report

Variant	rs12784228
Chromosome Location	chr10:91312337-91312338
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:91311732..91313706-chr10:91403897..91405980,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249962	Chromatin interaction
ENSG00000152782	Chromatin interaction
ENSG00000232936	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12765829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12778320	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1556610	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17123021	0.89[CEU][hapmap]
rs17123166	0.89[CEU][hapmap]
rs17123666	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17479692	0.94[CEU][hapmap]
rs34793067	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35296553	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35999721	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59089460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59415468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60158951	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66846065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71503888	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv1041964	chr10:90861380-91378356	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12784228	IFIT1	cis	cerebellum	SCAN
rs12784228	IFIT1	cis	parietal	SCAN
rs12784228	FLJ37201	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91305000-91315600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:91308800-91314000	Weak transcription	Pancreas	Pancrea
3	chr10:91310000-91312400	Weak transcription	HMEC	breast
4	chr10:91310400-91312600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr10:91310600-91312400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr10:91310600-91312400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr10:91310600-91312400	Weak transcription	NH-A	brain
8	chr10:91310800-91312400	Weak transcription	NHEK	skin
9	chr10:91310800-91313400	Weak transcription	Stomach Mucosa	stomach
10	chr10:91311000-91312400	Weak transcription	Osteobl	bone
11	chr10:91312200-91312400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr10:91312200-91312400	Bivalent Enhancer	NHDF-Ad	bronchial
13	chr10:91312200-91312600	Enhancers	Fetal Heart	heart
14	chr10:91312200-91312800	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr10:91312200-91312800	Enhancers	A549	lung
16	chr10:91312200-91313600	Enhancers	HSMMtube	muscle
17	chr10:91312200-91314200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr10:91312200-91314200	Enhancers	HSMM	muscle
19	chr10:91312200-91314600	Enhancers	Hela-S3	cervix
20	chr10:91312200-91314800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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