Variant report

Variant	rs17810870
Chromosome Location	chr2:57842453-57842454
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10496072	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11125726	0.84[ASN][1000 genomes]
rs17207557	0.85[ASN][1000 genomes]
rs17809425	0.89[CEU][hapmap];0.88[GIH][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes]
rs17812960	0.85[ASN][1000 genomes]
rs57173959	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57465834	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58220533	0.84[ASN][1000 genomes]
rs6759367	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs68008184	0.81[AMR][1000 genomes]
rs72935444	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72935446	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72948143	0.84[AMR][1000 genomes]
rs72948146	0.81[AMR][1000 genomes]
rs72950067	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559938	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999898	chr2:57193127-57901238	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535729	chr2:57193127-57901238	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1007118	chr2:57562051-58147588	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv834137	chr2:57683649-57913898	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv874193	chr2:57758608-58066673	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv874194	chr2:57793672-57896756	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv874195	chr2:57808671-57855341	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv1006688	chr2:57822953-58030203	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv527499	chr2:57842075-57845016	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv817984	chr2:57842075-57845016	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv20355	chr2:57842228-57849900	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17810870	CCDC104	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:57842200-57842600	Genic enhancers	Thymus	Thymus
2	chr2:57842200-57842800	Enhancers	Fetal Thymus	thymus

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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