Variant report

Variant	rs1699015
Chromosome Location	chr6:38572590-38572591
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38571505..38574322-chr6:38577217..38578879,2	K562	blood:
2	chr6:38567307..38570367-chr6:38570470..38574374,4	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10484854	1.00[CHB][hapmap]
rs10484856	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12154188	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12198212	1.00[CHB][hapmap]
rs12199427	0.85[GIH][hapmap];0.84[TSI][hapmap]
rs12206218	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12208087	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12214815	0.82[CHB][hapmap]
rs1406841	0.88[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1699013	0.85[CEU][hapmap]
rs1699014	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1699018	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1699020	0.85[CEU][hapmap]
rs17543429	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17622097	0.82[CHB][hapmap]
rs1781740	0.86[ASW][hapmap];0.92[CEU][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs1781741	0.85[CEU][hapmap]
rs1781742	0.93[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1937780	0.82[CHB][hapmap]
rs1997949	0.88[AMR][1000 genomes]
rs2748156	0.85[CEU][hapmap]
rs2748166	0.85[CEU][hapmap]
rs2748168	0.85[CEU][hapmap]
rs2748170	0.89[AFR][1000 genomes]
rs2748173	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs2814887	0.88[CEU][hapmap]
rs2814890	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs2814893	0.85[CEU][hapmap]
rs4254983	0.90[GIH][hapmap];0.84[TSI][hapmap]
rs6458060	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6903004	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6924443	0.85[CEU][hapmap]
rs6927145	0.81[CEU][hapmap]
rs7752239	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7755619	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7761154	0.81[CEU][hapmap]
rs7769186	0.85[CEU][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1699015	GLO1	cis	parietal	SCAN
rs1699015	ANKS1A	cis	cerebellum	SCAN
rs1699015	GLO1	cis	cerebellum	SCAN
rs1699015	MDFI	cis	cerebellum	SCAN
rs1699015	TAF11	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38535800-38578200	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:38556000-38580400	Weak transcription	Ovary	ovary
3	chr6:38557400-38578000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:38560600-38574400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:38560800-38580000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:38560800-38580200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:38561400-38577600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:38561400-38578000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:38562000-38574600	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:38562000-38578000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:38562200-38575000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:38562200-38580000	Weak transcription	Aorta	Aorta
13	chr6:38562800-38579800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:38564000-38580400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr6:38565000-38574800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr6:38565400-38589200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr6:38565800-38583200	Weak transcription	Primary T cells from cord blood	blood
18	chr6:38565800-38583600	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr6:38567800-38580400	Weak transcription	Right Ventricle	heart
20	chr6:38568200-38580000	Weak transcription	Psoas Muscle	Psoas
21	chr6:38568200-38584200	Weak transcription	Primary B cells from cord blood	blood
22	chr6:38571000-38580000	Weak transcription	Small Intestine	intestine
23	chr6:38571400-38577600	Weak transcription	Brain Hippocampus Middle	brain
24	chr6:38571600-38572600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:38571600-38573000	Enhancers	HSMMtube	muscle
26	chr6:38571600-38581800	Weak transcription	Left Ventricle	heart
27	chr6:38571800-38572800	Enhancers	Muscle Satellite Cultured Cells	--
28	chr6:38572000-38572600	Enhancers	NHLF	lung
29	chr6:38572000-38573600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr6:38572000-38577600	Weak transcription	Fetal Lung	lung
31	chr6:38572000-38578000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:38572000-38591600	Weak transcription	Fetal Intestine Small	intestine
33	chr6:38572200-38572600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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