Variant report

Variant	rs2559990
Chromosome Location	chr5:114921251-114921252
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:114884946..114886999-chr5:114921116..114924631,3	K562	blood:
2	chr5:114713336..114714974-chr5:114920219..114921988,2	MCF-7	breast:
3	chr5:114919821..114922254-chr5:114958227..114960432,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12187973	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs171773	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs171774	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs173965	0.82[ASN][1000 genomes]
rs173966	0.83[ASN][1000 genomes]
rs187682	0.91[ASN][1000 genomes]
rs2546486	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs2546487	0.90[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[ASN][1000 genomes]
rs256941	0.91[EUR][1000 genomes]
rs256943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs256944	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs256945	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs256956	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs256959	0.82[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs256962	1.00[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs256964	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs256967	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs256968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs256969	0.85[ASN][1000 genomes]
rs256970	0.82[ASN][1000 genomes]
rs256971	0.81[ASN][1000 genomes]
rs256972	0.81[ASN][1000 genomes]
rs256976	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.89[ASN][1000 genomes]
rs256980	0.93[ASN][1000 genomes]
rs256984	0.83[ASN][1000 genomes]
rs256986	0.82[ASN][1000 genomes]
rs256987	0.85[ASN][1000 genomes]
rs256988	0.85[ASN][1000 genomes]
rs256991	0.85[ASN][1000 genomes]
rs256993	0.85[ASN][1000 genomes]
rs256994	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs256996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs256997	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs256998	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs387718	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415577	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs416234	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs419939	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs424434	0.96[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs428191	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs712550	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs712551	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs790824	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs813761	0.90[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs9326969	1.00[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[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	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv830455	chr5:114761542-114938284	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1796164	chr5:114854685-114936768	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2559990	SEMA6A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114901400-114922400	Weak transcription	Fetal Muscle Leg	muscle
2	chr5:114910400-114925200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr5:114910400-114929400	Weak transcription	Adipose Nuclei	Adipose
4	chr5:114911200-114935600	Weak transcription	Gastric	stomach
5	chr5:114911800-114922400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr5:114912000-114924600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr5:114912200-114921400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:114913000-114935200	Weak transcription	Aorta	Aorta
9	chr5:114913600-114924400	Weak transcription	Placenta	Placenta
10	chr5:114914400-114936200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr5:114914800-114937400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:114915200-114924600	Weak transcription	Primary B cells from cord blood	blood
13	chr5:114915400-114921400	Weak transcription	Brain Anterior Caudate	brain
14	chr5:114915600-114924000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr5:114916400-114921400	Weak transcription	Lung	lung
16	chr5:114918600-114922800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:114918600-114922800	Enhancers	NHDF-Ad	bronchial
18	chr5:114919000-114921600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr5:114919200-114921600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:114919400-114930000	Weak transcription	HSMM	muscle
21	chr5:114919600-114921400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr5:114919600-114922000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:114919600-114923600	Weak transcription	Right Atrium	heart
24	chr5:114919600-114924400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:114919600-114924400	Weak transcription	Left Ventricle	heart
26	chr5:114919600-114924800	Weak transcription	Pancreas	Pancrea
27	chr5:114919800-114921400	Weak transcription	GM12878-XiMat	blood
28	chr5:114919800-114935600	Weak transcription	NH-A	brain
29	chr5:114920000-114929400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr5:114920000-114929600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:114920400-114921600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:114920400-114922000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:114920400-114922000	Enhancers	NHEK	skin
34	chr5:114920400-114929600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:114920600-114929600	Weak transcription	Osteobl	bone
36	chr5:114920800-114921600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:114920800-114922800	Enhancers	NHLF	lung
38	chr5:114921000-114921600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:114921000-114921600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:114921000-114921600	Enhancers	Fetal Heart	heart
41	chr5:114921000-114921600	Enhancers	Psoas Muscle	Psoas
42	chr5:114921000-114922000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:114921200-114921800	Strong transcription	Primary monocytes fromperipheralblood	blood

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