Variant report

Variant	rs2879544
Chromosome Location	chr10:52871733-52871734
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10508935	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10740130	0.83[TSI][hapmap]
rs10761807	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10761810	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10761811	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10761831	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10822189	0.82[EUR][1000 genomes]
rs10822194	0.82[EUR][1000 genomes]
rs10822197	0.96[EUR][1000 genomes]
rs10822198	0.82[EUR][1000 genomes]
rs10822210	0.84[EUR][1000 genomes]
rs10822211	0.84[EUR][1000 genomes]
rs10822229	0.82[EUR][1000 genomes]
rs10822230	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10995617	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10995620	0.84[EUR][1000 genomes]
rs10995651	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10995655	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10995673	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10995681	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12218335	0.81[EUR][1000 genomes]
rs12220644	0.84[EUR][1000 genomes]
rs12221226	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12415785	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16913900	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16913956	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2339675	0.82[EUR][1000 genomes]
rs7084128	0.81[EUR][1000 genomes]
rs7097311	0.81[EUR][1000 genomes]
rs7912628	0.81[EUR][1000 genomes]
rs9414805	0.94[EUR][1000 genomes]
rs9414807	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs9414809	0.93[EUR][1000 genomes]
rs9414810	0.81[EUR][1000 genomes]
rs9415709	0.81[EUR][1000 genomes]
rs9415710	0.81[EUR][1000 genomes]
rs9415711	0.81[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	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
3	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

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52844000-52877200	Weak transcription	Fetal Stomach	stomach
2	chr10:52856600-52877200	Weak transcription	Colon Smooth Muscle	Colon
3	chr10:52857600-52877200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr10:52858800-52873000	Weak transcription	Aorta	Aorta
5	chr10:52867400-52876400	Weak transcription	Left Ventricle	heart
6	chr10:52867600-52871800	Enhancers	NHDF-Ad	bronchial
7	chr10:52867600-52876000	Weak transcription	Psoas Muscle	Psoas
8	chr10:52869800-52871800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr10:52869800-52872000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr10:52870200-52872000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr10:52870400-52871800	Enhancers	NHLF	lung
12	chr10:52870400-52873000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr10:52870800-52876800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr10:52871200-52872000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr10:52871200-52872000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr10:52871200-52872200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr10:52871400-52872000	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr10:52871400-52876800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr10:52871600-52871800	Enhancers	H9 Cell Line	embryonic stem cell
20	chr10:52871600-52871800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr10:52871600-52872000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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