Variant report

Variant	rs6678795
Chromosome Location	chr1:169533266-169533267
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10753787	0.90[ASN][1000 genomes]
rs10800457	0.93[ASN][1000 genomes]
rs1894697	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1894698	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1894699	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1981491	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2040443	0.82[ASN][1000 genomes]
rs2187955	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239853	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3753305	0.93[ASN][1000 genomes]
rs4656188	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4656688	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4656689	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6427202	0.90[ASN][1000 genomes]
rs6670678	0.93[ASN][1000 genomes]
rs6685578	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540556	0.90[ASN][1000 genomes]
rs7548857	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs760694	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv548187	chr1:169530837-169559035	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv872534	chr1:169533266-169561274	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6678795	FAM48A	trans	cerebellum	SCAN
rs6678795	FMO6P	cis	parietal	SCAN
rs6678795	METTL13	cis	parietal	SCAN
rs6678795	DNAJB6	trans	parietal	SCAN
rs6678795	PBX1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169505800-169534800	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr1:169506200-169542800	Weak transcription	Right Ventricle	heart
3	chr1:169524600-169541800	Weak transcription	Placenta	Placenta
4	chr1:169528600-169533400	Weak transcription	Stomach Mucosa	stomach
5	chr1:169530200-169535400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:169530200-169539000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr1:169530400-169534000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr1:169530800-169534800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:169531600-169534800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:169532400-169534600	Strong transcription	Liver	Liver
11	chr1:169533000-169533600	ZNF genes & repeats	HepG2	liver
12	chr1:169533200-169551600	Strong transcription	Monocytes-CD14+_RO01746	blood

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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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