Variant report

Variant	rs10089078
Chromosome Location	chr8:39769939-39769940
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10089084	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10090859	0.87[ASN][1000 genomes]
rs10108662	0.82[CEU][hapmap];0.80[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10282745	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10282753	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11781681	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12155609	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13248037	0.91[ASN][1000 genomes]
rs13275363	0.92[ASN][1000 genomes]
rs13278716	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2340949	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28701100	0.92[ASN][1000 genomes]
rs28792440	0.88[ASN][1000 genomes]
rs28797203	0.89[ASN][1000 genomes]
rs35290228	0.91[ASN][1000 genomes]
rs35323275	0.93[ASN][1000 genomes]
rs5019014	0.88[ASN][1000 genomes]
rs6474188	0.91[ASN][1000 genomes]
rs6474193	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66531372	0.93[ASN][1000 genomes]
rs67257318	0.93[ASN][1000 genomes]
rs67692362	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68145761	0.93[ASN][1000 genomes]
rs6989949	0.91[ASN][1000 genomes]
rs6989954	0.91[ASN][1000 genomes]
rs6997491	0.91[ASN][1000 genomes]
rs7005763	0.87[ASN][1000 genomes]
rs7009740	0.80[ASN][1000 genomes]
rs7812568	0.91[ASN][1000 genomes]
rs7816174	0.91[ASN][1000 genomes]
rs7820268	0.82[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7824315	0.91[ASN][1000 genomes]
rs7825999	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7828521	0.91[ASN][1000 genomes]
rs7831046	0.89[ASN][1000 genomes]
rs7832494	0.91[ASN][1000 genomes]
rs7836577	0.82[CEU][hapmap];0.84[GIH][hapmap]
rs7838545	0.90[ASN][1000 genomes]
rs9693751	0.91[ASN][1000 genomes]
rs9693823	0.94[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	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	nsv508505	chr8:39730094-39791331	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1033371	chr8:39749437-39899540	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10089078	SLC20A2	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:39760200-39770400	Weak transcription	Right Atrium	heart
2	chr8:39762600-39771200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr8:39763200-39781600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr8:39763200-39783800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr8:39763400-39781000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr8:39763800-39780000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr8:39763800-39781800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr8:39765800-39773400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr8:39767800-39770400	Weak transcription	Hela-S3	cervix
10	chr8:39767800-39771200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr8:39768000-39770200	Weak transcription	Fetal Lung	lung
12	chr8:39768400-39771200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr8:39769000-39770600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr8:39769400-39770000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr8:39769600-39770200	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr8:39769800-39770000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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