Variant report

Variant	rs2150690
Chromosome Location	chr13:30109378-30109379
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1018679	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1018682	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10454590	0.81[TSI][hapmap]
rs12428026	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs1411928	0.87[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1571784	0.81[CEU][hapmap];0.80[GIH][hapmap]
rs166828	0.81[CHB][hapmap]
rs1877463	0.81[CHB][hapmap]
rs2150688	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183717	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2236499	0.95[CHB][hapmap]
rs2277451	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2776957	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2776959	0.87[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2776963	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802248	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280922	0.81[CHB][hapmap]
rs280923	0.85[CHB][hapmap]
rs280930	0.81[CHB][hapmap]
rs280933	0.81[CHB][hapmap]
rs280934	0.81[CHB][hapmap]
rs280936	0.81[CHB][hapmap]
rs2989594	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[ASN][1000 genomes]
rs3011605	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[ASN][1000 genomes]
rs3783248	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs3783257	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs3783259	1.00[CHB][hapmap]
rs3783260	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes]
rs3783262	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes]
rs3783263	1.00[CHB][hapmap]
rs3825536	1.00[CHB][hapmap]
rs476506	0.81[CHB][hapmap];0.90[MEX][hapmap]
rs579451	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap]
rs617892	0.81[CHB][hapmap]
rs6490409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs7997827	0.81[CHB][hapmap]
rs914362	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs9550481	0.91[ASN][1000 genomes]
rs9550482	0.90[CHB][hapmap];0.89[ASN][1000 genomes]
rs9551696	0.95[CHB][hapmap];0.90[ASN][1000 genomes]
rs9579383	0.86[TSI][hapmap]
rs9579384	0.86[TSI][hapmap]
rs9579386	0.86[TSI][hapmap]
rs9579388	0.86[TSI][hapmap]
rs9579389	0.86[TSI][hapmap]
rs9579390	0.86[TSI][hapmap]
rs9579393	0.86[TSI][hapmap]
rs9579398	0.81[TSI][hapmap]

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	nsv430551	chr13:30061100-30113000	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2150690	SHISA2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30071000-30128800	Strong transcription	Dnd41	blood
2	chr13:30082800-30111600	Weak transcription	Stomach Mucosa	stomach
3	chr13:30084200-30110400	Strong transcription	Fetal Intestine Small	intestine
4	chr13:30084200-30110600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr13:30084200-30112600	Strong transcription	NHEK	skin
6	chr13:30084200-30115800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr13:30084400-30111200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr13:30084600-30112200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr13:30084800-30110400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr13:30084800-30110600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr13:30084800-30111600	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr13:30085000-30111600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr13:30085600-30111200	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr13:30085600-30111600	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr13:30085800-30115400	Strong transcription	Primary T cells from cord blood	blood
16	chr13:30086000-30110600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr13:30086000-30111200	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr13:30087000-30110200	Strong transcription	GM12878-XiMat	blood
19	chr13:30089800-30110800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr13:30092200-30133000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr13:30095200-30112800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr13:30095400-30114800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr13:30095600-30110600	Strong transcription	Thymus	Thymus
24	chr13:30095800-30113200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr13:30096000-30110400	Strong transcription	NHLF	lung
26	chr13:30096000-30112600	Weak transcription	Psoas Muscle	Psoas
27	chr13:30096600-30112200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr13:30096800-30111600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr13:30096800-30112200	Weak transcription	Liver	Liver
30	chr13:30097200-30138400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr13:30098000-30117200	Weak transcription	Small Intestine	intestine
32	chr13:30098400-30110800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr13:30098800-30129000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr13:30099000-30114200	Weak transcription	Fetal Heart	heart
35	chr13:30100000-30110000	Strong transcription	NH-A	brain
36	chr13:30100200-30110600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr13:30100200-30111200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr13:30100400-30111400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr13:30100400-30112000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr13:30100600-30110600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr13:30100600-30110600	Strong transcription	Osteobl	bone
42	chr13:30100800-30109400	Strong transcription	Spleen	Spleen
43	chr13:30100800-30110400	Strong transcription	HepG2	liver
44	chr13:30100800-30110600	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr13:30100800-30110600	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr13:30100800-30111000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr13:30100800-30111800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr13:30101000-30110400	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr13:30101400-30111600	Strong transcription	HSMM	muscle
50	chr13:30102000-30110200	Strong transcription	HUVEC	blood vessel

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