Variant report

Variant	rs2929086
Chromosome Location	chr8:39948320-39948321
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10086014	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10086939	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10092175	0.92[EUR][1000 genomes]
rs10095401	0.84[EUR][1000 genomes]
rs10958600	0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs1383603	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1471559	0.95[CHB][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs1471560	0.83[ASW][hapmap];0.85[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs1471561	0.86[ASN][1000 genomes]
rs1481063	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2929077	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2929078	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2929080	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2929081	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2929082	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2929083	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2929084	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2929085	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2929095	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2955924	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2955925	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2955926	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2955927	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2981129	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2981134	0.88[EUR][1000 genomes]
rs2981136	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2981177	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2981178	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2981179	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4737039	0.90[ASN][1000 genomes]
rs7846287	0.91[ASN][1000 genomes]
rs9772008	0.81[AMR][1000 genomes];0.93[EUR][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	nsv539555	chr8:39683857-40673606	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv534582	chr8:39884590-40653224	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1034355	chr8:39942179-39961432	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2929086	STAR	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:39940000-39950000	Weak transcription	A549	lung
2	chr8:39944000-39950800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr8:39944200-39949800	Weak transcription	Colon Smooth Muscle	Colon
4	chr8:39944600-39950200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr8:39948200-39948400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr8:39948200-39948400	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr8:39948200-39948400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr8:39948200-39948600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:39948200-39948600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr8:39948200-39948600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr8:39948200-39948600	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr8:39948200-39948600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr8:39948200-39948600	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr8:39948200-39948800	Enhancers	HepG2	liver
15	chr8:39948200-39949000	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr8:39948200-39949200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr8:39948200-39949200	Enhancers	Stomach Mucosa	stomach
18	chr8:39948200-39950800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr8:39948200-39951000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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