Variant report

Variant	rs7925728
Chromosome Location	chr11:9013002-9013003
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9011431..9013216-chr11:9024076..9026448,2	MCF-7	breast:
2	chr11:9008310..9013368-chr11:9022083..9026889,11	K562	blood:
3	chr11:9010207..9011708-chr11:9012903..9015577,2	K562	blood:
4	chr11:9011525..9013427-chr11:9074733..9076584,2	K562	blood:

Variant related genes	Relation type
ENSG00000253973	Chromatin interaction
ENSG00000175352	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10743093	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs10743095	0.83[EUR][1000 genomes]
rs10769967	0.93[CEU][hapmap]
rs10769970	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10769971	0.87[JPT][hapmap]
rs10769973	0.93[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs10769978	0.86[EUR][1000 genomes]
rs10769979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769980	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769981	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10840130	0.84[CEU][hapmap]
rs10840134	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs10840141	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10840142	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10840147	0.89[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs10840148	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs10840157	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840158	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840160	0.83[CHD][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap]
rs11042078	0.89[CEU][hapmap]
rs11042103	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11042125	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs11042149	0.89[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11042150	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11042151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs11042152	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042154	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1109305	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1123936	0.93[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11603841	0.88[CEU][hapmap]
rs1529641	0.91[CEU][hapmap]
rs1560569	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs1980428	0.93[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1980429	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984791	0.83[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs2012680	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2012690	0.96[ASN][1000 genomes]
rs2012696	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2016942	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs2455603	0.86[YRI][hapmap]
rs2568020	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568021	0.93[YRI][hapmap]
rs2568027	0.82[YRI][hapmap]
rs2568043	0.92[CEU][hapmap]
rs2568045	0.93[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2568061	0.93[CEU][hapmap];0.86[MEX][hapmap]
rs2568065	0.93[CEU][hapmap];0.86[MEX][hapmap]
rs2568090	0.93[CEU][hapmap]
rs2653570	0.88[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2653588	0.82[YRI][hapmap]
rs2653605	0.88[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742470	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2742471	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742474	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742479	0.88[YRI][hapmap]
rs2742480	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2742518	0.82[YRI][hapmap]
rs2742537	0.83[CEU][hapmap]
rs2742540	0.85[CEU][hapmap]
rs2742545	0.85[CEU][hapmap]
rs2742552	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs4909952	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4910062	0.92[CEU][hapmap];0.80[JPT][hapmap]
rs4910156	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4910158	0.83[EUR][1000 genomes]
rs4910200	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4910442	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs4929922	0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6486060	0.92[CEU][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs7119939	0.92[CEU][hapmap]
rs7123429	0.93[CEU][hapmap]
rs7479407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7482838	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7484180	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7930026	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7937298	0.93[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap]
rs7945705	0.93[CEU][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv896984	chr11:8988550-9090408	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv896985	chr11:9013002-9152463	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs7925728	TMEM9B	cis	parietal	SCAN
rs7925728	TMEM9B-AS1	cis	lung	GTEx
rs7925728	OR52A1	cis	parietal	SCAN
rs7925728	WEE1	cis	parietal	SCAN
rs7925728	RRP8	cis	parietal	SCAN
rs7925728	NRIP3	cis	parietal	SCAN
rs7925728	RPL27A	cis	parietal	SCAN
rs7925728	ST5	cis	parietal	SCAN
rs7925728	TMEM9B-AS1	cis	Thyroid	GTEx
rs7925728	TMEM9B-AS1	cis	Esophagus Mucosa	GTEx
rs7925728	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs7925728	APBB1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8989600-9019600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:8991800-9015600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:9001800-9015200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:9011000-9023200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:9011800-9023000	Weak transcription	NHDF-Ad	bronchial
6	chr11:9012200-9013200	Weak transcription	K562	blood

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