Variant report

Variant	rs7560657
Chromosome Location	chr2:56032652-56032653
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:56021572..56023348-chr2:56031352..56033297,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10496051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496052	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11125601	0.91[ASN][1000 genomes]
rs11125602	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11125603	0.97[ASN][1000 genomes]
rs11125606	0.86[AMR][1000 genomes]
rs11893573	0.81[EUR][1000 genomes]
rs12464737	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12472893	0.91[ASN][1000 genomes]
rs12615158	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1344732	0.83[AMR][1000 genomes]
rs1346782	0.97[ASN][1000 genomes]
rs1346789	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1367225	0.83[AMR][1000 genomes]
rs1430190	0.81[AMR][1000 genomes]
rs1430202	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17047234	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17369648	0.84[AMR][1000 genomes]
rs1946545	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985160	0.81[AMR][1000 genomes]
rs1985162	0.83[AMR][1000 genomes]
rs1985163	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2009262	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3791675	0.95[CEU][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes]
rs3791679	0.95[CEU][hapmap];0.95[MEX][hapmap];0.90[AMR][1000 genomes]
rs4146921	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4146922	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4347871	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58027672	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58680090	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59556444	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59985551	0.88[AMR][1000 genomes]
rs62164463	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62167713	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545522	0.98[ASN][1000 genomes]
rs6715773	0.80[YRI][hapmap]
rs6724369	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732132	0.82[AMR][1000 genomes]
rs7563032	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7574127	0.81[AMR][1000 genomes]
rs7591694	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9753383	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7560657	ASB3	cis	cerebellum	SCAN
rs7560657	EFEMP1	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56029600-56037000	Weak transcription	Hela-S3	cervix
2	chr2:56030600-56034000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr2:56031000-56033000	Enhancers	Adipose Nuclei	Adipose
4	chr2:56031200-56033600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr2:56031600-56033200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:56031600-56033200	Enhancers	Fetal Brain Male	brain
7	chr2:56031800-56033000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:56031800-56033000	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr2:56031800-56033200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:56032000-56033600	Enhancers	Aorta	Aorta
11	chr2:56032000-56033600	Enhancers	Brain Anterior Caudate	brain
12	chr2:56032000-56036800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:56032000-56036800	Weak transcription	A549	lung
14	chr2:56032000-56039800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:56032200-56033000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:56032200-56033600	Enhancers	Brain Substantia Nigra	brain
17	chr2:56032200-56036800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:56032200-56036800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr2:56032200-56036800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:56032400-56032800	Weak transcription	Brain Germinal Matrix	brain
21	chr2:56032600-56033400	Enhancers	Fetal Brain Female	brain
22	chr2:56032600-56033800	Enhancers	Brain Hippocampus Middle	brain

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