Variant report

Variant	rs3099370
Chromosome Location	chr10:61696597-61696598
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1008887	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10740000	0.84[ASN][1000 genomes]
rs1171849	0.81[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1184593	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1626088	0.80[CHB][hapmap]
rs1664256	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs1664275	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1684913	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099371	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479670	0.90[ASN][1000 genomes]
rs6479675	0.81[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7893603	0.90[ASN][1000 genomes]
rs978353	0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1800316	chr10:61639599-61700473	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3099370	CCDC6	cis	Esophagus Mucosa	GTEx
rs3099370	SLC16A9	cis	cerebellum	SCAN
rs3099370	EGR2	cis	parietal	SCAN
rs3099370	HLA-L	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:61695600-61696600	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr10:61695600-61696600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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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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