Variant report

Variant	rs6473635
Chromosome Location	chr8:52566493-52566494
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13261618	0.97[EUR][1000 genomes]
rs13263610	1.00[CEU][hapmap]
rs13277070	1.00[CEU][hapmap]
rs17210431	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap]
rs17210466	1.00[CEU][hapmap]
rs17282351	1.00[CEU][hapmap]
rs34424720	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[MEX][hapmap]
rs4471027	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4577950	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932026	chr8:51858658-52758574	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv890895	chr8:52190571-52615191	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS 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	22 gene(s)	inside rSNPs	diseases
4	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers 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	19 gene(s)	inside rSNPs	diseases
5	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats 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	19 gene(s)	inside rSNPs	diseases
6	nsv831313	chr8:52458835-52638968	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6473635	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52559600-52570400	Weak transcription	Left Ventricle	heart
2	chr8:52560400-52567800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr8:52562800-52568600	Enhancers	Fetal Heart	heart
4	chr8:52563400-52573400	Weak transcription	Right Atrium	heart
5	chr8:52564000-52567600	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr8:52564800-52567000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr8:52565200-52567800	Weak transcription	Fetal Brain Male	brain
8	chr8:52565800-52566800	Enhancers	Adipose Nuclei	Adipose
9	chr8:52565800-52566800	Enhancers	Fetal Lung	lung
10	chr8:52566200-52566600	Enhancers	Ovary	ovary
11	chr8:52566200-52566600	Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr8:52566200-52566800	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr8:52566200-52566800	Enhancers	Psoas Muscle	Psoas
14	chr8:52566400-52566800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr8:52566400-52567200	Enhancers	Colon Smooth Muscle	Colon
16	chr8:52566400-52580800	Weak transcription	Aorta	Aorta

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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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