Variant report

Variant	rs2128817
Chromosome Location	chr8:54815801-54815802
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:54813329..54816016-chr8:54818127..54820294,2	K562	blood:
2	chr8:54805478..54808027-chr8:54814864..54817596,2	K562	blood:
3	chr8:54806250..54809119-chr8:54814470..54816413,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10504159	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11984932	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap]
rs11992921	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap]
rs1483537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16919584	1.00[CEU][hapmap]
rs16919648	1.00[CEU][hapmap]
rs16919650	1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs16919652	1.00[CEU][hapmap]
rs16919653	1.00[CEU][hapmap];0.93[CHD][hapmap];0.84[AMR][1000 genomes]
rs16919658	1.00[CEU][hapmap]
rs16919683	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs16919694	1.00[CEU][hapmap]
rs1905359	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs2128816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2128818	0.84[AMR][1000 genomes]
rs2128819	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs57204839	1.00[ASN][1000 genomes]
rs58344188	1.00[ASN][1000 genomes]
rs59939582	1.00[ASN][1000 genomes]
rs60594961	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61054351	1.00[ASN][1000 genomes]
rs6473896	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs7005604	1.00[CEU][hapmap]
rs73587686	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73680353	0.84[AMR][1000 genomes]
rs73680356	0.84[AMR][1000 genomes]
rs7821073	1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[TSI][hapmap]
rs7838182	1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[TSI][hapmap]
rs936685	1.00[CEU][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2128817	RGS20	cis	lymphoblastoid	seeQTL
rs2128817	LMCD1	trans	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:54803400-54817200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr8:54804000-54816000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr8:54807000-54816200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:54808000-54816000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr8:54809600-54818200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr8:54810600-54816000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr8:54810600-54816400	Weak transcription	Brain Anterior Caudate	brain
8	chr8:54811800-54817200	Weak transcription	Fetal Brain Female	brain
9	chr8:54812600-54816000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr8:54813400-54816000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr8:54814000-54816000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr8:54814200-54816600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr8:54814400-54816400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr8:54814600-54816400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr8:54814800-54816000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr8:54815000-54816400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr8:54815000-54816600	Genic enhancers	NHEK	skin
18	chr8:54815200-54816600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr8:54815400-54816600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr8:54815800-54816000	Flanking Active TSS	GM12878-XiMat	blood
21	chr8:54815800-54816600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr8:54815800-54816600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr8:54815800-54816600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr8:54815800-54816600	Genic enhancers	A549	lung
25	chr8:54815800-54816600	Enhancers	HMEC	breast
26	chr8:54815800-54819800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr8:54815800-54819800	Enhancers	NHLF	lung
28	chr8:54815800-54819800	Enhancers	Osteobl	bone
29	chr8:54815800-54820000	Enhancers	Muscle Satellite Cultured Cells	--
30	chr8:54815800-54821000	Enhancers	NHDF-Ad	bronchial

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