Variant report

Variant	rs60104228
Chromosome Location	chr5:59787858-59787859
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10514893	0.85[EUR][1000 genomes]
rs10514894	0.85[EUR][1000 genomes]
rs10939848	0.94[ASN][1000 genomes]
rs1423471	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1423473	0.96[ASN][1000 genomes]
rs16877933	0.85[EUR][1000 genomes]
rs16877936	0.85[EUR][1000 genomes]
rs16877964	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16877967	0.93[EUR][1000 genomes]
rs16878035	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878037	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878086	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878104	0.96[ASN][1000 genomes]
rs16878106	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16878108	0.94[ASN][1000 genomes]
rs17326404	0.93[EUR][1000 genomes]
rs17378750	0.93[EUR][1000 genomes]
rs1862589	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2409102	0.94[ASN][1000 genomes]
rs3763059	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4090603	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55737169	0.94[ASN][1000 genomes]
rs55952213	0.89[EUR][1000 genomes]
rs56151644	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56217581	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56247947	0.89[EUR][1000 genomes]
rs56262275	0.89[EUR][1000 genomes]
rs57177718	0.89[EUR][1000 genomes]
rs58376959	1.00[EUR][1000 genomes]
rs58512371	0.89[EUR][1000 genomes]
rs58594585	0.85[EUR][1000 genomes]
rs58704174	0.89[EUR][1000 genomes]
rs58891299	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59014679	0.89[EUR][1000 genomes]
rs59313902	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59576667	0.89[EUR][1000 genomes]
rs59578756	0.89[EUR][1000 genomes]
rs60257457	0.94[ASN][1000 genomes]
rs60962155	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61166140	0.91[ASN][1000 genomes]
rs61379877	0.94[ASN][1000 genomes]
rs61474228	0.93[EUR][1000 genomes]
rs6449471	0.94[ASN][1000 genomes]
rs6878429	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6881782	0.85[EUR][1000 genomes]
rs6886423	0.93[EUR][1000 genomes]
rs6891858	0.96[ASN][1000 genomes]
rs73106781	0.89[EUR][1000 genomes]
rs73106782	0.89[EUR][1000 genomes]
rs73108627	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73108631	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73108666	0.93[ASN][1000 genomes]
rs73108670	0.94[ASN][1000 genomes]
rs73108674	0.94[ASN][1000 genomes]
rs73759052	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73759053	1.00[EUR][1000 genomes]
rs7702188	0.85[EUR][1000 genomes]
rs7702474	0.96[ASN][1000 genomes]
rs7705194	0.96[ASN][1000 genomes]
rs7712662	0.93[ASN][1000 genomes]
rs7723861	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7725629	1.00[EUR][1000 genomes]
rs7734108	0.94[ASN][1000 genomes]
rs7737086	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv598297	chr5:59734004-59862453	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59767200-59789000	Weak transcription	Primary B cells from cord blood	blood
2	chr5:59782000-59801000	Weak transcription	Fetal Brain Male	brain
3	chr5:59784200-59790600	Weak transcription	Brain Anterior Caudate	brain
4	chr5:59784600-59788800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:59784600-59789000	Weak transcription	NHDF-Ad	bronchial
6	chr5:59784600-59791200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:59784600-59791800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:59784600-59794200	Weak transcription	Gastric	stomach
9	chr5:59784800-59788800	Weak transcription	Stomach Mucosa	stomach
10	chr5:59784800-59793600	Weak transcription	Colon Smooth Muscle	Colon
11	chr5:59785000-59788800	Weak transcription	HSMM	muscle
12	chr5:59785200-59788800	Weak transcription	Osteobl	bone
13	chr5:59785200-59791800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:59785200-59793400	Weak transcription	Fetal Stomach	stomach
15	chr5:59785600-59789000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:59785600-59789000	Weak transcription	HMEC	breast
17	chr5:59785800-59791000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:59786000-59790800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr5:59786400-59789800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr5:59786600-59788800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:59786600-59788800	Weak transcription	Aorta	Aorta
22	chr5:59786600-59790000	Weak transcription	Brain Hippocampus Middle	brain
23	chr5:59787000-59788800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:59787000-59788800	Weak transcription	NHEK	skin
25	chr5:59787200-59789400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr5:59787200-59789800	Weak transcription	Brain Angular Gyrus	brain
27	chr5:59787200-59790200	Weak transcription	Brain Substantia Nigra	brain
28	chr5:59787200-59793400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:59787400-59788800	Weak transcription	A549	lung
30	chr5:59787400-59789400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:59787600-59791200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr5:59787800-59788400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr5:59787800-59788800	Weak transcription	HepG2	liver

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