Variant report

Variant	rs1369678
Chromosome Location	chr2:52147979-52147980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10865259	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11125396	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12995692	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13031702	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1435800	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62139968	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545243	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6711598	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6712451	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs737022	0.92[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap]
rs7592931	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs984093	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009513	chr2:51890060-52821980	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv431047	chr2:51961737-52263543	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1013553	chr2:52010500-52471153	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv535712	chr2:52010500-52471153	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv874094	chr2:52068507-52153668	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv874095	chr2:52074452-52174187	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1004603	chr2:52083910-52265663	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv526141	chr2:52096257-52262932	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv999607	chr2:52096309-52263162	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1013892	chr2:52102670-52263231	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv1013459	chr2:52107116-52155835	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv1014342	chr2:52114176-52378299	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	esv1808238	chr2:52126166-52150034	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1369678	C2orf63	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:52144800-52148000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr2:52146400-52148200	Enhancers	Hela-S3	cervix
3	chr2:52147600-52148200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:52147800-52151400	Weak transcription	Osteobl	bone

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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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