Variant report

Variant	rs16919653
Chromosome Location	chr8:54810167-54810168
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:54799455..54801202-chr8:54809079..54811926,2	K562	blood:

Variant related genes	Relation type
ENSG00000244159	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10504159	1.00[CEU][hapmap]
rs11984932	1.00[CEU][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs11985444	0.96[ASN][1000 genomes]
rs11992921	1.00[CEU][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs1483537	1.00[CEU][hapmap]
rs16919584	1.00[CEU][hapmap]
rs16919648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs16919650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16919652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16919655	0.93[ASN][1000 genomes]
rs16919658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16919683	1.00[CEU][hapmap]
rs16919694	1.00[CEU][hapmap]
rs1905359	1.00[CEU][hapmap]
rs2128816	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs2128817	1.00[CEU][hapmap];0.93[CHD][hapmap];0.84[AMR][1000 genomes]
rs2128818	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2128819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2220093	0.82[YRI][hapmap]
rs60594961	0.84[AMR][1000 genomes]
rs6473896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7005604	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs73587686	0.81[AMR][1000 genomes]
rs73680353	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73680356	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7821073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs7821757	0.96[ASN][1000 genomes]
rs7838182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.86[MKK][hapmap];0.86[YRI][hapmap];0.96[ASN][1000 genomes]
rs936685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021775	chr8:54631303-54827173	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv539621	chr8:54631303-54827173	Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1023983	chr8:54790309-55145770	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv539623	chr8:54790309-55145770	Bivalent Enhancer Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16919653	RGS20	cis	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:54798400-54814600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr8:54799400-54812200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr8:54799800-54812400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr8:54800400-54810600	Weak transcription	HMEC	breast
5	chr8:54803400-54817200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr8:54803800-54811600	Weak transcription	A549	lung
7	chr8:54804000-54816000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr8:54807000-54816200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:54807800-54813200	Weak transcription	NHLF	lung
10	chr8:54807800-54815800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr8:54808000-54810400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr8:54808000-54810800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr8:54808000-54810800	Weak transcription	NHEK	skin
14	chr8:54808000-54816000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr8:54808800-54815000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr8:54809000-54811200	Weak transcription	Fetal Brain Female	brain
17	chr8:54809600-54818200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr8:54809800-54810600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr8:54809800-54810800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr8:54809800-54815200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr8:54810000-54810400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr8:54810000-54810600	Enhancers	GM12878-XiMat	blood
23	chr8:54810000-54813200	Weak transcription	NHDF-Ad	bronchial

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