Variant report

Variant	rs16916968
Chromosome Location	chr8:52844411-52844412
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10087958	0.81[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10453128	0.82[ASN][1000 genomes]
rs1589079	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16916966	0.80[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2138297	0.90[ASN][1000 genomes]
rs2176119	0.90[ASN][1000 genomes]
rs6473666	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7813414	0.98[ASN][1000 genomes]
rs7816834	0.82[ASN][1000 genomes]
rs7817558	0.82[ASN][1000 genomes]
rs7817892	0.82[ASN][1000 genomes]
rs7819892	1.00[ASN][1000 genomes]
rs7820177	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7833668	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[ASN][1000 genomes]
rs7834181	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7838307	0.84[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs877248	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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	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
2	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
3	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16916968	PCMTD1	cis	brain	seeQTL
rs16916968	PCMTD1	cis	cerebellum	SCAN
rs16916968	C11orf63	trans	parietal	SCAN
rs16916968	LOC115294	cis	multi-tissue	Pritchard
rs16916968	PCMTD1	trans	brain	seeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52814200-52850000	Weak transcription	Spleen	Spleen
2	chr8:52815000-52852000	Weak transcription	Colon Smooth Muscle	Colon
3	chr8:52822600-52860200	Weak transcription	Fetal Muscle Leg	muscle
4	chr8:52831800-52858400	Weak transcription	Primary T cells from cord blood	blood
5	chr8:52831800-52863400	Weak transcription	Aorta	Aorta
6	chr8:52837800-52851800	Weak transcription	Ovary	ovary
7	chr8:52838000-52853400	Weak transcription	Esophagus	oesophagus
8	chr8:52841600-52852000	Weak transcription	Lung	lung
9	chr8:52841800-52844600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr8:52841800-52845200	Weak transcription	Psoas Muscle	Psoas
11	chr8:52842200-52845800	Weak transcription	Right Atrium	heart
12	chr8:52842200-52851800	Weak transcription	Left Ventricle	heart
13	chr8:52842400-52850800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr8:52842600-52851000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr8:52844200-52845200	Enhancers	Pancreas	Pancrea

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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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