Variant report

Variant	rs17543178
Chromosome Location	chr6:38543377-38543378
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38542387..38543937-chr6:38555368..38558343,2	K562	blood:
2	chr6:38542008..38544985-chr6:38545718..38547507,2	K562	blood:
3	chr6:38535111..38538464-chr6:38540181..38544221,3	MCF-7	breast:
4	chr6:38538560..38540420-chr6:38542934..38544675,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10498741	0.83[CEU][hapmap];0.81[GIH][hapmap]
rs12214815	0.87[YRI][hapmap]
rs1569853	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17542411	0.83[CEU][hapmap];0.90[GIH][hapmap]
rs17544359	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17544798	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2180106	1.00[CHB][hapmap]
rs2748174	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs55835070	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56133825	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57180089	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57327719	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58167057	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61330823	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73733936	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73733937	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73733941	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73733942	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73733956	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73733958	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73733961	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73733984	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73733987	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73733989	0.85[EUR][1000 genomes]
rs73733992	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73733994	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73733996	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73734417	1.00[ASN][1000 genomes]
rs73734424	1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17543178	GLO1	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38510600-38546800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:38519600-38554800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:38523000-38571600	Weak transcription	HSMMtube	muscle
4	chr6:38532400-38547800	Weak transcription	Fetal Kidney	kidney
5	chr6:38533000-38544000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr6:38533200-38547000	Weak transcription	Aorta	Aorta
7	chr6:38534200-38544800	Weak transcription	Fetal Intestine Large	intestine
8	chr6:38534400-38544400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr6:38534400-38561600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr6:38534800-38547000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr6:38535400-38554600	Weak transcription	Fetal Stomach	stomach
12	chr6:38535600-38543600	Weak transcription	Ovary	ovary
13	chr6:38535600-38543600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:38535600-38544800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:38535600-38547000	Weak transcription	Brain Substantia Nigra	brain
16	chr6:38535600-38547000	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:38535600-38555400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:38535600-38555800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:38535600-38556000	Weak transcription	Brain Hippocampus Middle	brain
20	chr6:38535600-38556000	Weak transcription	NHLF	lung
21	chr6:38535600-38557600	Weak transcription	HSMM	muscle
22	chr6:38535800-38543800	Weak transcription	Adipose Nuclei	Adipose
23	chr6:38535800-38544200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:38535800-38547800	Weak transcription	Osteobl	bone
25	chr6:38535800-38548000	Weak transcription	Fetal Heart	heart
26	chr6:38535800-38559800	Weak transcription	Fetal Lung	lung
27	chr6:38535800-38560200	Weak transcription	NH-A	brain
28	chr6:38535800-38564000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:38535800-38578200	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:38536000-38546800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:38536200-38556000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:38536200-38559200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:38536400-38544000	Weak transcription	Psoas Muscle	Psoas
34	chr6:38536400-38555800	Weak transcription	NHDF-Ad	bronchial
35	chr6:38536400-38560200	Weak transcription	Brain Angular Gyrus	brain
36	chr6:38536800-38566400	Weak transcription	Pancreas	Pancrea
37	chr6:38537000-38557200	Weak transcription	Thymus	Thymus
38	chr6:38538000-38566800	Weak transcription	Esophagus	oesophagus
39	chr6:38538200-38558600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr6:38538400-38544200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr6:38538600-38548000	Weak transcription	Fetal Intestine Small	intestine
42	chr6:38538600-38561800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr6:38538600-38562000	Weak transcription	Brain Germinal Matrix	brain
44	chr6:38539000-38545800	Weak transcription	Brain Anterior Caudate	brain
45	chr6:38539800-38545800	Weak transcription	Left Ventricle	heart
46	chr6:38539800-38554800	Weak transcription	Lung	lung
47	chr6:38539800-38562800	Weak transcription	Fetal Thymus	thymus
48	chr6:38540000-38548000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:38540200-38544800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:38540200-38547800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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