Variant report

Variant	rs7128670
Chromosome Location	chr11:103904556-103904557
allele	A/C/G/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	RFX5	chr11:103903673-103904870	SK-N-SH	brain:	n/a	chr11:103904111-103904120

Variant related genes	Relation type
DDI1	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10750683	0.95[YRI][hapmap]
rs11600096	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11824542	1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12805893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1483501	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs17331699	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs17332348	1.00[CHB][hapmap]
rs1818106	0.83[MKK][hapmap];0.95[YRI][hapmap]
rs2279789	1.00[YRI][hapmap]
rs2515081	1.00[CHB][hapmap]
rs260808	0.82[GIH][hapmap]
rs260847	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260854	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260855	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34987759	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35016460	1.00[ASN][1000 genomes]
rs35965296	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs496339	1.00[CHD][hapmap]
rs55966490	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs589796	1.00[CHB][hapmap]
rs67576530	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7102675	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7113370	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7121786	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs72975261	0.89[ASN][1000 genomes]
rs7927365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9326345	0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2750977	chr11:103082558-103924790	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv948974	chr11:103082558-103932207	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv2760322	chr11:103760085-104374141	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1051448	chr11:103864766-104274112	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv541157	chr11:103864766-104274112	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1043976	chr11:103881236-104526403	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7128670	CASP4	cis	cerebellum	SCAN
rs7128670	CASP4	cis	Skin Sun Exposed Lower leg	GTEx
rs7128670	MMP7	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:103889400-103907000	Weak transcription	Pancreas	Pancrea
2	chr11:103896600-103914000	Weak transcription	Gastric	stomach
3	chr11:103897000-103909600	Weak transcription	Aorta	Aorta
4	chr11:103902200-103922800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr11:103903400-103905400	Enhancers	Fetal Intestine Large	intestine
6	chr11:103903600-103904600	Weak transcription	Fetal Intestine Small	intestine
7	chr11:103903800-103904600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:103904000-103904600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr11:103904000-103905000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:103904000-103905000	Enhancers	Fetal Lung	lung
11	chr11:103904000-103905400	Enhancers	Ovary	ovary
12	chr11:103904000-103906000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:103904000-103906200	Enhancers	Fetal Heart	heart
14	chr11:103904200-103904600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr11:103904200-103904600	Enhancers	Muscle Satellite Cultured Cells	--
16	chr11:103904400-103904600	Flanking Active TSS	A549	lung
17	chr11:103904400-103905800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:103904400-103906000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr11:103904400-103909400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links