Variant report

Variant	rs1321056
Chromosome Location	chr6:38535576-38535577
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38535241..38537591-chr6:38552081..38553699,2	MCF-7	breast:
2	chr6:38535111..38538464-chr6:38540181..38544221,3	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10807196	0.96[CEU][hapmap];0.81[CHD][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs10807198	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10947752	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1699001	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1699002	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1699003	1.00[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1699004	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1699005	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1699007	1.00[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1699017	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1739621	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1739626	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1739627	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs1739628	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1739629	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1739630	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1739632	1.00[CEU][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1739633	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1781708	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1781711	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1781712	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1852979	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2092797	0.83[CHD][hapmap]
rs2144328	0.89[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2180104	0.80[EUR][1000 genomes]
rs2252550	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2748165	0.82[EUR][1000 genomes]
rs2748172	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2814883	0.92[CEU][hapmap];0.83[CHD][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs2814885	0.83[EUR][1000 genomes]
rs2814889	0.92[CEU][hapmap];0.81[CHD][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs2814894	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4392718	0.96[CEU][hapmap];0.81[CHD][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs6458059	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6931131	0.83[CHD][hapmap]
rs6932235	0.81[CHD][hapmap]
rs910516	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9394508	0.81[CHD][hapmap]
rs9394521	0.88[EUR][1000 genomes];0.86[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1321056	GLO1	cis	parietal	SCAN
rs1321056	DNAH8	cis	cerebellum	SCAN
rs1321056	GLO1	cis	cerebellum	SCAN
rs1321056	BYSL	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38496600-38539600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:38497000-38538800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr6:38497000-38539400	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr6:38510600-38546800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:38513000-38539200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:38514200-38539400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:38515600-38535800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:38516000-38538800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr6:38519200-38538800	Weak transcription	Primary T cells from cord blood	blood
10	chr6:38519200-38539400	Weak transcription	Left Ventricle	heart
11	chr6:38519600-38554800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:38523000-38571600	Weak transcription	HSMMtube	muscle
13	chr6:38524000-38537400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:38524000-38539200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:38532200-38539600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:38532400-38547800	Weak transcription	Fetal Kidney	kidney
17	chr6:38532800-38538200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr6:38533000-38544000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr6:38533200-38537800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:38533200-38547000	Weak transcription	Aorta	Aorta
21	chr6:38533400-38536200	Enhancers	Brain Germinal Matrix	brain
22	chr6:38533600-38536400	Enhancers	Fetal Brain Male	brain
23	chr6:38533800-38535600	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr6:38533800-38536200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:38534000-38535600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:38534000-38535600	Enhancers	HUVEC	blood vessel
27	chr6:38534000-38536000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr6:38534000-38539200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:38534200-38535800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:38534200-38535800	Enhancers	NH-A	brain
31	chr6:38534200-38536000	Enhancers	Fetal Brain Female	brain
32	chr6:38534200-38536400	Enhancers	Brain Angular Gyrus	brain
33	chr6:38534200-38536400	Enhancers	NHDF-Ad	bronchial
34	chr6:38534200-38539600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:38534200-38544800	Weak transcription	Fetal Intestine Large	intestine
36	chr6:38534400-38535600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:38534400-38535600	Enhancers	Brain Cingulate Gyrus	brain
38	chr6:38534400-38535600	Enhancers	Brain Hippocampus Middle	brain
39	chr6:38534400-38535600	Enhancers	HSMM	muscle
40	chr6:38534400-38535800	Enhancers	Fetal Lung	lung
41	chr6:38534400-38535800	Enhancers	Osteobl	bone
42	chr6:38534400-38536000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:38534400-38544400	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr6:38534400-38561600	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr6:38534600-38535600	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr6:38534800-38535600	Enhancers	NHLF	lung
47	chr6:38534800-38535800	Enhancers	Fetal Heart	heart
48	chr6:38534800-38536200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:38534800-38536800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr6:38534800-38537600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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