Variant report

Variant	rs9516648
Chromosome Location	chr13:96895842-96895843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1072563	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12428610	0.81[EUR][1000 genomes]
rs16953068	0.87[ASN][1000 genomes]
rs1925115	0.86[ASN][1000 genomes]
rs1925122	0.87[ASN][1000 genomes]
rs1927790	0.90[ASN][1000 genomes]
rs1927804	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1927805	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1927807	0.81[EUR][1000 genomes]
rs1927808	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1927809	0.81[EUR][1000 genomes]
rs1930219	0.89[AMR][1000 genomes]
rs1930223	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2149316	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2149317	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2149318	0.81[EUR][1000 genomes]
rs2182987	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2389629	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4771932	0.87[ASN][1000 genomes]
rs61966875	0.88[ASN][1000 genomes]
rs6491285	0.87[ASN][1000 genomes]
rs7320065	0.88[ASN][1000 genomes]
rs7323056	0.85[ASN][1000 genomes]
rs7324113	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7328389	0.82[EUR][1000 genomes]
rs7337506	0.88[ASN][1000 genomes]
rs748457	0.90[ASN][1000 genomes]
rs7981845	0.88[ASN][1000 genomes]
rs7981931	0.90[ASN][1000 genomes]
rs7984912	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7987636	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7997409	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8002865	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9302095	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9302097	0.80[EUR][1000 genomes]
rs9302098	0.80[EUR][1000 genomes]
rs9516642	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9516649	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9516651	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9516653	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9525158	0.83[TSI][hapmap];0.86[YRI][hapmap];0.80[EUR][1000 genomes]
rs9525166	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9525169	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9525171	0.89[AMR][1000 genomes]
rs9554333	0.90[ASN][1000 genomes]
rs9556550	0.83[ASN][1000 genomes]
rs9556551	0.87[ASN][1000 genomes]
rs9556554	0.83[ASN][1000 genomes]
rs9556555	0.86[ASN][1000 genomes]
rs9562060	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1041165	chr13:96522021-96966520	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv869471	chr13:96622327-97223956	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv530390	chr13:96681439-97193029	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
6	nsv900936	chr13:96697209-97032483	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv1136	chr13:96892691-96937795	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9516648	CLDN10	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96895400-96896000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr13:96895600-96896000	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr13:96895600-96897800	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr13:96895800-96896000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr13:96895800-96899800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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