Variant report

Variant	rs7016385
Chromosome Location	chr8:10779472-10779473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10090444	0.82[EUR][1000 genomes]
rs10107145	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10110723	1.00[JPT][hapmap]
rs11250092	1.00[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11250093	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11250094	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1139843	1.00[JPT][hapmap]
rs11776368	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs11777007	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11783247	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap]
rs11783749	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11990550	1.00[CHB][hapmap]
rs11993591	1.00[CHB][hapmap]
rs12542037	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs12546366	0.90[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap]
rs12548184	0.83[AMR][1000 genomes]
rs2409692	1.00[CHB][hapmap]
rs34741518	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073948	0.89[EUR][1000 genomes]
rs4240671	0.95[MEX][hapmap];0.87[TSI][hapmap]
rs4240673	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap]
rs4326350	0.85[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs4520127	1.00[CHB][hapmap]
rs4554431	0.83[ASN][1000 genomes]
rs4841457	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4841458	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs4841460	1.00[CHB][hapmap]
rs4841461	1.00[JPT][hapmap]
rs4841465	0.81[CEU][hapmap]
rs6984496	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6985109	0.92[CEU][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6988281	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6992103	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7005884	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7015168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7823296	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7833435	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7837038	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7843470	0.85[CEU][hapmap];0.83[AMR][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	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active 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	37 gene(s)	inside rSNPs	diseases
2	nsv1017836	chr8:10591801-10803617	Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1034988	chr8:10591801-10804243	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1025190	chr8:10756331-10802566	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7016385	CLDN23	cis	multi-tissue	Pritchard
rs7016385	C8orf13	cis	multi-tissue	Pritchard

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10778400-10780600	ZNF genes & repeats	Pancreas	Pancrea
2	chr8:10778600-10779600	ZNF genes & repeats	Fetal Brain Female	brain
3	chr8:10778600-10780400	ZNF genes & repeats	Brain Germinal Matrix	brain
4	chr8:10778800-10779600	ZNF genes & repeats	Brain Angular Gyrus	brain
5	chr8:10778800-10780400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr8:10779200-10780800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr8:10779400-10780000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
8	chr8:10779400-10780200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr8:10779400-10785400	Weak transcription	Brain Anterior Caudate	brain
10	chr8:10779400-10785600	Weak transcription	Brain Inferior Temporal Lobe	brain

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