Variant report

Variant	rs10282572
Chromosome Location	chr7:87674671-87674672
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10235694	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10241669	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10266440	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10279744	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10279940	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10435251	0.81[EUR][1000 genomes]
rs10952906	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11770982	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11972409	0.96[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12669586	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12704375	0.88[EUR][1000 genomes]
rs12704380	0.96[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12704381	0.93[EUR][1000 genomes]
rs1613737	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1623535	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs1629569	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs1631368	0.92[EUR][1000 genomes]
rs1637487	0.94[EUR][1000 genomes]
rs1637488	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs1637489	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs1637492	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1637494	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1637495	0.83[EUR][1000 genomes]
rs1637496	0.92[EUR][1000 genomes]
rs1637497	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs1637498	0.92[EUR][1000 genomes]
rs1637499	0.96[CEU][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs1637500	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs1637502	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs1637503	0.92[CEU][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs1637504	0.88[EUR][1000 genomes]
rs1637505	0.86[EUR][1000 genomes]
rs1637506	0.88[EUR][1000 genomes]
rs1637508	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1688886	0.96[CEU][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs1688887	0.93[EUR][1000 genomes]
rs1688888	0.96[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1688890	0.96[CEU][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs1688891	0.96[CEU][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1688893	0.93[EUR][1000 genomes]
rs1688894	0.93[EUR][1000 genomes]
rs1688895	0.93[EUR][1000 genomes]
rs1688896	0.93[EUR][1000 genomes]
rs1688897	0.93[EUR][1000 genomes]
rs1688898	0.94[EUR][1000 genomes]
rs1688899	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs1688901	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs1688902	0.96[CEU][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs17150161	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2021741	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2022160	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2022163	0.96[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2022164	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2022555	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs2023533	0.96[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2024018	0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2024019	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2079422	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2079423	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2097917	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2108087	0.96[CEU][hapmap]
rs2158766	0.96[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2282948	0.96[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2282949	0.96[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2282951	0.85[CEU][hapmap]
rs2282955	0.82[CHB][hapmap]
rs2299190	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs2373486	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2373487	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28432284	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28794871	0.87[EUR][1000 genomes]
rs4728718	0.90[EUR][1000 genomes]
rs4728731	0.82[CHB][hapmap]
rs56050913	0.80[EUR][1000 genomes]
rs56160917	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56897831	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58850563	0.80[EUR][1000 genomes]
rs59135798	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60069756	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62486383	0.80[EUR][1000 genomes]
rs6465124	0.87[EUR][1000 genomes]
rs6465126	0.81[EUR][1000 genomes]
rs6465127	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7786538	0.87[EUR][1000 genomes]
rs7802934	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7803521	0.93[EUR][1000 genomes]
rs7809391	0.82[EUR][1000 genomes]
rs9641021	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9641022	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]

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	nsv888677	chr7:86802025-87781111	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1015862	chr7:87075394-88049798	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1023352	chr7:87418818-88192925	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv539005	chr7:87418818-88192925	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv525073	chr7:87535096-87812968	Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv437021	chr7:87666666-87674671	Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10282572	RNF125	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:87670600-87675000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:87671400-87674800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr7:87671800-87675000	Weak transcription	Brain Angular Gyrus	brain
4	chr7:87672000-87674800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr7:87672200-87674800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr7:87672200-87674800	Weak transcription	Adipose Nuclei	Adipose
7	chr7:87672200-87674800	Weak transcription	Brain Anterior Caudate	brain
8	chr7:87672200-87674800	Weak transcription	Brain Hippocampus Middle	brain
9	chr7:87672400-87674800	Weak transcription	GM12878-XiMat	blood
10	chr7:87673000-87675400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr7:87674000-87675000	Enhancers	Fetal Intestine Large	intestine
12	chr7:87674400-87674800	Enhancers	Duodenum Mucosa	Duodenum
13	chr7:87674400-87675000	Enhancers	Fetal Intestine Small	intestine
14	chr7:87674400-87675000	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr7:87674400-87675800	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr7:87674600-87674800	Enhancers	Liver	Liver
17	chr7:87674600-87675800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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