Variant report

Variant	rs10863664
Chromosome Location	chr1:222027190-222027191
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11118874	0.86[EUR][1000 genomes]
rs11118875	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118052	0.82[EUR][1000 genomes]
rs12130910	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35090621	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4308986	0.88[CEU][hapmap];0.95[EUR][1000 genomes]
rs4384245	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4528124	0.88[CEU][hapmap];0.89[GIH][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs6604675	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604676	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6604677	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6658977	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6659311	0.83[EUR][1000 genomes]
rs6691170	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6699132	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544478	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550628	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7556214	0.81[EUR][1000 genomes]
rs7556228	0.81[AMR][1000 genomes];0.84[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	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10863664	CCDC137	trans	cerebellum	SCAN
rs10863664	AIDA	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222019800-222031800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:222019800-222047600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:222020200-222029600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:222020600-222031600	Weak transcription	HMEC	breast
5	chr1:222025400-222028600	Weak transcription	NHLF	lung
6	chr1:222025400-222029200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:222025400-222031800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:222025400-222031800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:222025800-222028200	Weak transcription	NHDF-Ad	bronchial
10	chr1:222025800-222029800	Weak transcription	Hela-S3	cervix
11	chr1:222026400-222028200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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Input of quick search could be:

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

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