Variant report

Variant	rs2593590
Chromosome Location	chr11:15841326-15841327
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:15792043..15792613-chr11:15841089..15841866,2	MCF-7	breast:
2	chr11:15839247..15841645-chr11:15844030..15847018,3	K562	blood:
3	chr11:15792503..15793055-chr11:15841188..15841874,2	K562	blood:
4	chr11:15671338..15672254-chr11:15840920..15841521,2	MCF-7	breast:
5	chr11:15650817..15651581-chr11:15841314..15841899,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1009460	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832522	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832523	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11023754	0.87[MEX][hapmap]
rs12226568	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12272146	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12786929	0.84[ASN][1000 genomes]
rs12800617	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1348076	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440708	0.95[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1440709	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1465893	0.84[ASN][1000 genomes]
rs1543832	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1837605	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1882129	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1882130	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1882132	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920666	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920667	0.88[ASW][hapmap];0.95[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1920668	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920669	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920670	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1920671	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920672	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1960710	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165355	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593588	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593589	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2615041	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2615042	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2615043	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7101476	0.84[ASN][1000 genomes]
rs7106776	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051187	chr11:15781277-15846536	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv832073	chr11:15822409-15984078	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2593590	MYOD1	cis	parietal	SCAN
rs2593590	DKK3	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:15829800-15848000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:15836600-15841800	Enhancers	Adipose Nuclei	Adipose
3	chr11:15837600-15841800	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr11:15838000-15841400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:15838200-15841400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr11:15838800-15841400	Weak transcription	Right Atrium	heart
7	chr11:15838800-15847000	Weak transcription	Pancreas	Pancrea
8	chr11:15838800-15848000	Weak transcription	Left Ventricle	heart
9	chr11:15839000-15841400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:15839000-15841400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr11:15839000-15841400	Weak transcription	HMEC	breast
12	chr11:15839000-15841600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr11:15839000-15843000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:15839000-15845000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr11:15839400-15841400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr11:15839400-15841800	Enhancers	Colon Smooth Muscle	Colon
17	chr11:15839400-15845000	Weak transcription	NH-A	brain
18	chr11:15839400-15850200	Weak transcription	Aorta	Aorta
19	chr11:15839600-15841400	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr11:15839600-15841600	Enhancers	Fetal Intestine Large	intestine
21	chr11:15839800-15841800	Enhancers	Stomach Mucosa	stomach
22	chr11:15839800-15842000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr11:15839800-15845600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:15839800-15845600	Weak transcription	Osteobl	bone
25	chr11:15839800-15847400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr11:15840000-15841800	Enhancers	Liver	Liver
27	chr11:15840200-15841400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr11:15840200-15841600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr11:15840200-15841600	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr11:15840400-15842000	Enhancers	Brain Anterior Caudate	brain
31	chr11:15840600-15841600	Enhancers	Duodenum Mucosa	Duodenum
32	chr11:15840600-15841600	Enhancers	Right Ventricle	heart
33	chr11:15840600-15842000	Enhancers	Brain Hippocampus Middle	brain
34	chr11:15840800-15841400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr11:15840800-15841400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr11:15840800-15841400	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr11:15841000-15841400	Weak transcription	Brain Angular Gyrus	brain
38	chr11:15841000-15841400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr11:15841000-15842000	Enhancers	Brain Substantia Nigra	brain
40	chr11:15841000-15842000	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr11:15841200-15841600	Enhancers	Fetal Muscle Leg	muscle
42	chr11:15841200-15841600	Enhancers	NHEK	skin
43	chr11:15841200-15842000	Enhancers	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links