Variant report

Variant	rs2814889
Chromosome Location	chr6:38519761-38519762
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10807196	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10807198	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs10947740	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs10947752	0.83[EUR][1000 genomes]
rs1321056	0.92[CEU][hapmap];0.81[CHD][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs1699001	0.92[CEU][hapmap]
rs1699002	0.92[CEU][hapmap];0.90[TSI][hapmap]
rs1699003	0.84[ASW][hapmap];0.92[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs1699007	0.84[ASW][hapmap];0.92[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs1699017	0.81[EUR][1000 genomes]
rs1739626	0.92[CEU][hapmap];0.90[TSI][hapmap]
rs1739627	0.92[CEU][hapmap]
rs1739628	0.80[EUR][1000 genomes]
rs1739629	0.80[EUR][1000 genomes]
rs1739632	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1739633	0.83[CHD][hapmap]
rs1781708	0.92[CEU][hapmap];0.90[TSI][hapmap]
rs1852979	0.83[EUR][1000 genomes]
rs2092797	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs2144328	0.81[CEU][hapmap]
rs2180104	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2252550	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs2474245	0.84[ASN][1000 genomes]
rs2748157	0.82[ASN][1000 genomes]
rs2748164	0.89[ASN][1000 genomes]
rs2748165	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2748172	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2814883	0.84[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2814885	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2814894	0.84[ASW][hapmap];0.92[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs4392718	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55949948	0.89[ASN][1000 genomes]
rs6458059	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs6923737	0.86[CHB][hapmap];0.88[MKK][hapmap]
rs6931131	0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs6932235	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs7740763	0.82[JPT][hapmap]
rs910516	0.92[CEU][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs9394508	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2814889	BYSL	cis	cerebellum	SCAN
rs2814889	GLO1	cis	parietal	SCAN
rs2814889	GLO1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38494400-38524200	Weak transcription	Aorta	Aorta
2	chr6:38494800-38522600	Weak transcription	Ovary	ovary
3	chr6:38495000-38521800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr6:38496600-38539600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:38496800-38521600	Weak transcription	Lung	lung
6	chr6:38497000-38538800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr6:38497000-38539400	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr6:38500800-38520800	Weak transcription	Fetal Intestine Small	intestine
9	chr6:38508200-38522200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:38510200-38522200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:38510400-38522600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:38510600-38546800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:38511600-38522800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:38513000-38522400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr6:38513000-38539200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:38514200-38539400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr6:38515600-38535800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:38516000-38538800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr6:38517800-38519800	Weak transcription	Fetal Heart	heart
20	chr6:38517800-38535000	Weak transcription	Brain Substantia Nigra	brain
21	chr6:38518000-38522200	Weak transcription	HSMMtube	muscle
22	chr6:38518400-38520600	Enhancers	Primary B cells from cord blood	blood
23	chr6:38518600-38521200	Enhancers	Primary B cells from peripheral blood	blood
24	chr6:38518800-38521200	Weak transcription	Right Atrium	heart
25	chr6:38519000-38520800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr6:38519200-38538800	Weak transcription	Primary T cells from cord blood	blood
27	chr6:38519200-38539400	Weak transcription	Left Ventricle	heart
28	chr6:38519400-38520200	Enhancers	Primary hematopoietic stem cells	blood
29	chr6:38519400-38520600	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr6:38519600-38519800	Enhancers	GM12878-XiMat	blood
31	chr6:38519600-38520200	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr6:38519600-38520400	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr6:38519600-38554800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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