Variant report

Variant	rs10508935
Chromosome Location	chr10:52866503-52866504
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10740111	0.80[EUR][1000 genomes]
rs10740130	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10761738	0.87[EUR][1000 genomes]
rs10761807	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761810	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10761811	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10761831	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10822188	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10822189	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10822194	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10822197	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10822198	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10822210	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10822211	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10822229	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10822230	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10995458	0.87[EUR][1000 genomes]
rs10995473	0.82[EUR][1000 genomes]
rs10995526	0.88[EUR][1000 genomes]
rs10995617	0.83[AMR][1000 genomes]
rs10995620	0.81[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];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10995655	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10995673	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10995681	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10995788	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10995790	0.91[ASN][1000 genomes]
rs12218335	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12220644	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12221226	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12415785	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12767015	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16913257	0.87[EUR][1000 genomes]
rs16913900	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16913956	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1983222	0.85[EUR][1000 genomes]
rs2339675	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2660202	0.88[EUR][1000 genomes]
rs2666543	0.86[EUR][1000 genomes]
rs2879544	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3964605	0.88[EUR][1000 genomes]
rs55767509	0.87[EUR][1000 genomes]
rs7074892	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7084128	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7084767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7097311	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7912628	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9299457	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9414806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9414808	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9414810	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9415709	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9415710	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9415711	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9633564	0.86[EUR][1000 genomes]

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	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
4	nsv825378	chr10:52855771-52908439	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10508935	IFI44L	trans	lymphoblastoid	seeQTL
rs10508935	IFIT1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52844000-52877200	Weak transcription	Fetal Stomach	stomach
2	chr10:52853000-52871200	Weak transcription	Fetal Muscle Leg	muscle
3	chr10:52856600-52877200	Weak transcription	Colon Smooth Muscle	Colon
4	chr10:52857600-52877200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr10:52858800-52873000	Weak transcription	Aorta	Aorta
6	chr10:52864200-52869000	Weak transcription	HUVEC	blood vessel
7	chr10:52864400-52868200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr10:52864400-52868400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr10:52864800-52870200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr10:52865600-52867200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr10:52865600-52867200	Enhancers	NHDF-Ad	bronchial
12	chr10:52865800-52866600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr10:52865800-52866600	Enhancers	NHLF	lung
14	chr10:52866000-52868600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr10:52866200-52867400	Enhancers	Left Ventricle	heart
16	chr10:52866200-52867600	Enhancers	Psoas Muscle	Psoas
17	chr10:52866400-52866600	Enhancers	NH-A	brain
18	chr10:52866400-52866800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr10:52866400-52868200	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links