Variant report

Variant	rs10938086
Chromosome Location	chr4:74396706-74396707
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10011419	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10016403	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10019146	1.00[CEU][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10019320	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10020054	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10021827	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10028196	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10028276	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10029673	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10518115	0.90[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10805065	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10938077	0.82[EUR][1000 genomes]
rs10938078	0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs10938079	0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs10938085	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11728915	0.80[EUR][1000 genomes]
rs11943798	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1247668	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1247670	0.90[CEU][hapmap]
rs1247671	0.90[CEU][hapmap]
rs12503916	1.00[CEU][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12504448	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12505842	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12506668	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12506675	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12507775	1.00[CEU][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12508661	0.90[CEU][hapmap]
rs12508974	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12510629	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12510870	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs13103378	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13120998	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13144296	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13353732	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1358592	0.86[MEX][hapmap];0.81[EUR][1000 genomes]
rs1528915	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1528916	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1528917	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1528918	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1528924	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1569204	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1590115	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1590116	0.87[EUR][1000 genomes]
rs16849628	1.00[CEU][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16849629	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16849651	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16849656	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16849659	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16849675	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16849677	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16849727	0.90[CEU][hapmap];0.91[TSI][hapmap]
rs17192413	0.90[CEU][hapmap]
rs1745300	0.81[MEX][hapmap]
rs1881611	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1919469	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1919479	0.87[EUR][1000 genomes]
rs1997332	0.81[EUR][1000 genomes]
rs1997333	0.82[EUR][1000 genomes]
rs2008288	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2040354	0.81[EUR][1000 genomes]
rs2071097	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2141465	0.82[EUR][1000 genomes]
rs2141470	0.86[EUR][1000 genomes]
rs2178290	0.82[EUR][1000 genomes]
rs2178292	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2204736	0.89[EUR][1000 genomes]
rs28407399	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28450939	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28612539	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28693538	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34238679	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34773614	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34832471	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34859660	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35988516	0.89[EUR][1000 genomes]
rs3756073	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4235119	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs4267703	0.82[EUR][1000 genomes]
rs4267704	0.82[EUR][1000 genomes]
rs4267705	0.82[EUR][1000 genomes]
rs4438732	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4574378	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4618279	0.87[EUR][1000 genomes]
rs4631010	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4694170	1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4694173	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56011127	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56384466	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6446937	0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs6446938	0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs6446941	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6838329	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6852149	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72647083	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72649103	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7665563	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7665972	0.87[EUR][1000 genomes]
rs7667019	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7667185	0.87[EUR][1000 genomes]
rs7674913	0.87[EUR][1000 genomes]
rs7676460	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7676850	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7676870	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7676884	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7682201	1.00[CEU][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7687216	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7695792	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7695946	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7696502	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9990707	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9999939	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]

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	esv3430875	chr4:74243646-74420354	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv3364178	chr4:74383966-74400177	Enhancers Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10938086	RCHY1	cis	parietal	SCAN
rs10938086	MUC7	cis	cerebellum	SCAN
rs10938086	ART3	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74374600-74399000	Weak transcription	Fetal Intestine Large	intestine
2	chr4:74390400-74399800	Weak transcription	Fetal Intestine Small	intestine
3	chr4:74394200-74400000	Genic enhancers	Liver	Liver

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