Variant report

Variant	rs10090638
Chromosome Location	chr8:19673750-19673751
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10092840	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11204077	0.84[CEU][hapmap]
rs12547934	0.87[EUR][1000 genomes]
rs13280085	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2083640	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2083641	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3758061	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3855754	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4392917	0.87[EUR][1000 genomes]
rs4464983	0.87[EUR][1000 genomes]
rs6982084	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6986456	1.00[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs7012694	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7823457	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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	nsv890625	chr8:19368697-19799641	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv610759	chr8:19561997-20068842	Enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv3425950	chr8:19673522-19676520	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10090638	INTS10	cis	multi-tissue	Pritchard
rs10090638	NAT2	cis	parietal	SCAN
rs10090638	INTS10	cis	parietal	SCAN
rs10090638	NAT1	cis	cerebellum	SCAN
rs10090638	INTS10	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19670600-19673800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr8:19670600-19673800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:19670600-19674000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:19671400-19674000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr8:19672400-19674200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr8:19673600-19673800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr8:19673600-19673800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr8:19673600-19673800	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr8:19673600-19673800	Enhancers	Dnd41	blood
10	chr8:19673600-19673800	Enhancers	Hela-S3	cervix
11	chr8:19673600-19673800	Enhancers	Osteobl	bone
12	chr8:19673600-19674000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr8:19673600-19674000	Enhancers	Brain Hippocampus Middle	brain
14	chr8:19673600-19674000	Flanking Active TSS	A549	lung
15	chr8:19673600-19674000	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr8:19673600-19674400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
17	chr8:19673600-19675800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr8:19673600-19675800	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr8:19673600-19676000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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