Variant report

Variant	rs2339675
Chromosome Location	chr10:52852610-52852611
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10508935	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10740111	0.83[EUR][1000 genomes]
rs10740130	0.92[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10761738	0.90[EUR][1000 genomes]
rs10761807	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10761810	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10761811	0.83[AMR][1000 genomes]
rs10761831	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10822188	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10822189	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10822194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10822197	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10822198	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10822210	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10822211	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10822229	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10995458	0.90[EUR][1000 genomes]
rs10995473	0.85[EUR][1000 genomes]
rs10995526	0.90[EUR][1000 genomes]
rs10995617	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10995620	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10995651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10995655	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10995788	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10995790	0.85[ASN][1000 genomes]
rs12218335	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12220644	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12221226	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12415785	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12767015	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16913257	0.90[EUR][1000 genomes]
rs16913900	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16913956	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1983222	0.87[EUR][1000 genomes]
rs2660202	0.90[EUR][1000 genomes]
rs2666543	0.89[EUR][1000 genomes]
rs2879544	0.82[EUR][1000 genomes]
rs3964605	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4622210	0.82[EUR][1000 genomes]
rs55767509	0.90[EUR][1000 genomes]
rs7074892	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7084128	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7084767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7097311	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7912628	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9299457	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9414805	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9414806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9414807	0.80[EUR][1000 genomes]
rs9414808	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9414809	0.81[EUR][1000 genomes]
rs9414810	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9415709	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9415710	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9415711	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9633564	0.89[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	nsv831873	chr10:52710610-52899540	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv895394	chr10:52793177-52866503	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1036645	chr10:52804961-53159076	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2339675	IFIT1	trans	lymphoblastoid	seeQTL
rs2339675	NCOA4	cis	parietal	SCAN
rs2339675	SGMS1	cis	lymphoblastoid	seeQTL
rs2339675	IFI44L	trans	lymphoblastoid	seeQTL
rs2339675	OAS1	trans	lymphoblastoid	seeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52843600-52856200	Weak transcription	Aorta	Aorta
2	chr10:52844000-52877200	Weak transcription	Fetal Stomach	stomach
3	chr10:52849400-52853200	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr10:52849600-52853800	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr10:52850200-52863400	Weak transcription	NHLF	lung
6	chr10:52851600-52852800	Enhancers	Colon Smooth Muscle	Colon
7	chr10:52851800-52852800	Enhancers	Rectal Smooth Muscle	rectum
8	chr10:52852000-52853000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr10:52852000-52853200	Enhancers	Brain Substantia Nigra	brain
10	chr10:52852200-52853000	Enhancers	Fetal Brain Male	brain
11	chr10:52852200-52853000	Enhancers	Fetal Muscle Leg	muscle
12	chr10:52852200-52853000	Enhancers	Left Ventricle	heart
13	chr10:52852200-52853000	Enhancers	Psoas Muscle	Psoas
14	chr10:52852200-52853200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr10:52852200-52853200	Enhancers	Right Atrium	heart
16	chr10:52852200-52853400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr10:52852200-52853400	Enhancers	Adipose Nuclei	Adipose
18	chr10:52852200-52853800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr10:52852200-52855600	Weak transcription	Fetal Heart	heart
20	chr10:52852400-52852800	Active TSS	Stomach Smooth Muscle	stomach
21	chr10:52852400-52853000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr10:52852400-52853000	Weak transcription	Fetal Lung	lung
23	chr10:52852400-52856800	Weak transcription	Ovary	ovary
24	chr10:52852600-52852800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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