Variant report

Variant	rs16916979
Chromosome Location	chr8:52853501-52853502
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10086504	0.95[CHB][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10087958	0.91[YRI][hapmap]
rs10092494	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10097328	0.95[CHB][hapmap]
rs10102568	0.84[ASN][1000 genomes]
rs10504132	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs10958308	0.85[CHB][hapmap];0.92[EUR][1000 genomes]
rs11992148	0.92[EUR][1000 genomes]
rs12115132	0.83[ASN][1000 genomes]
rs13281179	0.95[CHB][hapmap]
rs16916878	0.87[CHB][hapmap]
rs16916903	0.81[ASN][1000 genomes]
rs16916968	0.83[YRI][hapmap]
rs16916974	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16917021	0.92[EUR][1000 genomes]
rs16917071	0.92[EUR][1000 genomes]
rs16917074	0.92[EUR][1000 genomes]
rs16917075	0.92[EUR][1000 genomes]
rs2020431	0.81[ASN][1000 genomes]
rs2090258	0.92[EUR][1000 genomes]
rs28754887	0.96[ASN][1000 genomes]
rs4873623	0.92[EUR][1000 genomes]
rs55713338	0.92[EUR][1000 genomes]
rs56275645	0.92[EUR][1000 genomes]
rs57745642	0.92[EUR][1000 genomes]
rs59734823	0.92[EUR][1000 genomes]
rs61196861	0.85[ASN][1000 genomes]
rs61262162	0.92[EUR][1000 genomes]
rs7009037	0.92[EUR][1000 genomes]
rs7010217	0.95[CHB][hapmap]
rs7011046	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs73592226	0.81[ASN][1000 genomes]
rs7815751	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7843530	0.82[ASN][1000 genomes]
rs877248	0.81[YRI][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16916979	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52822600-52860200	Weak transcription	Fetal Muscle Leg	muscle
2	chr8:52831800-52858400	Weak transcription	Primary T cells from cord blood	blood
3	chr8:52831800-52863400	Weak transcription	Aorta	Aorta
4	chr8:52850000-52860400	Weak transcription	Right Ventricle	heart
5	chr8:52850200-52860200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr8:52850200-52868000	Weak transcription	Primary B cells from cord blood	blood
7	chr8:52852000-52853600	Enhancers	Lung	lung
8	chr8:52852000-52870000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr8:52852200-52853600	Enhancers	GM12878-XiMat	blood
10	chr8:52852200-52858400	Weak transcription	Pancreas	Pancrea
11	chr8:52852200-52858800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr8:52852200-52859200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr8:52852200-52859400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr8:52852200-52866000	Weak transcription	Left Ventricle	heart
15	chr8:52852400-52854400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr8:52852400-52856600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr8:52852600-52861000	Weak transcription	Adipose Nuclei	Adipose
18	chr8:52852600-52862400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr8:52852600-52867600	Weak transcription	Fetal Kidney	kidney
20	chr8:52852800-52861000	Weak transcription	Fetal Stomach	stomach
21	chr8:52852800-52867000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr8:52853000-52853600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr8:52853000-52853600	Enhancers	NHEK	skin
24	chr8:52853000-52853800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr8:52853000-52856400	Weak transcription	Psoas Muscle	Psoas
26	chr8:52853200-52853600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr8:52853200-52853600	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr8:52853400-52853600	Enhancers	Esophagus	oesophagus

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