Variant report

Variant	rs6865466
Chromosome Location	chr5:146709917-146709918
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10065495	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs10074141	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10476886	1.00[AMR][1000 genomes]
rs10476887	1.00[AMR][1000 genomes]
rs1424294	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17106455	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28478946	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6879511	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7701219	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015804	chr5:146066000-146788233	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv537915	chr5:146066000-146788233	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv519847	chr5:146166378-146812647	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv599938	chr5:146169511-146806365	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv869238	chr5:146179403-146787986	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6865466	FAM25B	trans	lymphoblastoid	seeQTL
rs6865466	FAM25G	trans	lymphoblastoid	seeQTL
rs6865466	FAM25C	trans	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146703200-146711800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:146703600-146716400	Weak transcription	Ovary	ovary
3	chr5:146703800-146711400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:146707000-146716400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:146707400-146716400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:146707600-146725600	Weak transcription	Pancreas	Pancrea
7	chr5:146707800-146712000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr5:146709000-146711600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:146709800-146710000	Enhancers	Brain Germinal Matrix	brain
10	chr5:146709800-146710000	Enhancers	Fetal Kidney	kidney

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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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