Variant report

Variant	rs6924443
Chromosome Location	chr6:38486878-38486879
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38033550..38035424-chr6:38486236..38488883,2	MCF-7	breast:
2	chr6:38480377..38484448-chr6:38485640..38487510,3	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1073900	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs10947742	0.90[JPT][hapmap]
rs10947749	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs10947750	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs12193868	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs12198294	0.81[CEU][hapmap]
rs12199427	0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs12206371	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs1699015	0.85[CEU][hapmap]
rs1699018	0.85[CEU][hapmap]
rs1781740	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs1781742	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs2748156	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2748161	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2748173	1.00[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs2814882	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2814887	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2814890	1.00[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs4074421	0.80[EUR][1000 genomes]
rs4141854	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs4236061	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4254983	0.81[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs4631264	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs55869483	0.84[EUR][1000 genomes]
rs56083119	0.83[EUR][1000 genomes]
rs56250767	0.84[EUR][1000 genomes]
rs6458060	0.85[CEU][hapmap]
rs6938737	0.81[JPT][hapmap]
rs724242	0.90[JPT][hapmap]
rs72853429	0.80[EUR][1000 genomes]
rs7752972	0.83[ASN][1000 genomes]
rs7753374	0.83[ASN][1000 genomes]
rs7761154	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767041	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs9296252	0.90[JPT][hapmap]
rs9357277	0.90[JPT][hapmap]
rs9366965	0.83[ASN][1000 genomes]
rs9369065	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9394513	0.82[ASN][1000 genomes]
rs9394514	0.82[ASN][1000 genomes]
rs9394515	0.90[JPT][hapmap]
rs9462439	0.83[ASN][1000 genomes]
rs9462441	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs9462442	0.90[JPT][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6924443	GLO1	cis	cerebellum	SCAN
rs6924443	GLO1	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38444600-38496200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr6:38452400-38496600	Weak transcription	Primary B cells from cord blood	blood
3	chr6:38471600-38493200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:38472000-38493800	Weak transcription	Lung	lung
5	chr6:38476600-38499800	Weak transcription	Pancreas	Pancrea
6	chr6:38476800-38498800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:38477800-38498400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:38478000-38494800	Weak transcription	Fetal Kidney	kidney
9	chr6:38479000-38509800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:38480400-38489800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:38482600-38493800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:38483200-38493600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:38483600-38493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:38485000-38487000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:38485000-38487600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:38485000-38489800	Weak transcription	Brain Anterior Caudate	brain
17	chr6:38485200-38492200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:38485200-38496200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr6:38485400-38487800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:38485400-38489600	Weak transcription	Fetal Stomach	stomach
21	chr6:38485400-38489600	Weak transcription	Left Ventricle	heart
22	chr6:38485400-38489600	Weak transcription	Psoas Muscle	Psoas
23	chr6:38485400-38489600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:38485400-38489800	Weak transcription	Fetal Lung	lung
25	chr6:38485400-38489800	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:38485400-38489800	Weak transcription	Ovary	ovary
27	chr6:38485400-38489800	Weak transcription	Right Atrium	heart
28	chr6:38485400-38489800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr6:38485400-38493600	Weak transcription	Fetal Intestine Small	intestine
30	chr6:38485400-38493800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:38485400-38500400	Weak transcription	Gastric	stomach
32	chr6:38485600-38490400	Weak transcription	Small Intestine	intestine
33	chr6:38485600-38493800	Weak transcription	Fetal Intestine Large	intestine
34	chr6:38485800-38489600	Weak transcription	Colon Smooth Muscle	Colon
35	chr6:38485800-38489800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:38485800-38493800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr6:38485800-38495600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:38486000-38487000	Enhancers	HUVEC	blood vessel
39	chr6:38486000-38493600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:38486200-38487000	Enhancers	Primary B cells from peripheral blood	blood
41	chr6:38486200-38487800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr6:38486400-38487000	Enhancers	Primary T cells from cord blood	blood
43	chr6:38486400-38487000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr6:38486400-38487400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr6:38486400-38487600	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr6:38486400-38487600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr6:38486400-38493800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:38486400-38495600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr6:38486600-38487400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr6:38486600-38487600	Enhancers	Primary T helper cells PMA-I stimulated	--

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