Variant report

Variant	rs2748156
Chromosome Location	chr6:38513174-38513175
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

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

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]
rs2748161	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2748173	1.00[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs2814882	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[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]
rs4236061	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4254983	0.81[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs4631264	0.90[JPT][hapmap]
rs55869483	0.84[EUR][1000 genomes]
rs56083119	0.83[EUR][1000 genomes]
rs56250767	0.84[EUR][1000 genomes]
rs6458060	0.85[CEU][hapmap]
rs6924443	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]
rs6938737	0.81[JPT][hapmap]
rs724242	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs72853429	0.80[EUR][1000 genomes]
rs7761154	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7767041	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs9296252	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9357277	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9369065	0.90[JPT][hapmap]
rs9394514	0.81[ASN][1000 genomes]
rs9394515	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9462441	0.81[JPT][hapmap]
rs9462442	0.90[JPT][hapmap];0.83[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2748156	GLO1	cis	parietal	SCAN
rs2748156	GLO1	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38487000-38518600	Weak transcription	Primary T cells from cord blood	blood
2	chr6:38494400-38513800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr6:38494400-38515400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:38494400-38518800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:38494400-38524200	Weak transcription	Aorta	Aorta
6	chr6:38494800-38522600	Weak transcription	Ovary	ovary
7	chr6:38495000-38521800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr6:38496200-38517600	Weak transcription	Esophagus	oesophagus
9	chr6:38496600-38539600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:38496800-38521600	Weak transcription	Lung	lung
11	chr6:38497000-38517600	Weak transcription	Small Intestine	intestine
12	chr6:38497000-38538800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr6:38497000-38539400	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr6:38498400-38518400	Weak transcription	Primary B cells from cord blood	blood
15	chr6:38500600-38514800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:38500600-38517600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:38500600-38517600	Weak transcription	Right Ventricle	heart
18	chr6:38500600-38518600	Weak transcription	Left Ventricle	heart
19	chr6:38500800-38520800	Weak transcription	Fetal Intestine Small	intestine
20	chr6:38501400-38518600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr6:38506800-38517000	Weak transcription	Brain Anterior Caudate	brain
22	chr6:38508200-38522200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:38510200-38522200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:38510400-38522600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:38510600-38546800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:38511600-38517000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:38511600-38522800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:38511800-38516800	Weak transcription	Fetal Stomach	stomach
29	chr6:38512000-38517200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr6:38512200-38519000	Weak transcription	Fetal Intestine Large	intestine
31	chr6:38512200-38519000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:38512400-38519400	Weak transcription	Fetal Muscle Leg	muscle
33	chr6:38512600-38515200	Weak transcription	Placenta	Placenta
34	chr6:38512800-38513200	Enhancers	K562	blood
35	chr6:38513000-38522400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:38513000-38539200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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