Variant report

Variant	rs2748173
Chromosome Location	chr6:38530142-38530143
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1073900	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10947749	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10947750	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12193868	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12198294	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199427	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[ASN][1000 genomes]
rs12206371	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1406841	0.85[CHD][hapmap]
rs1699015	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs1699018	0.85[CEU][hapmap];0.85[CHD][hapmap];0.84[TSI][hapmap]
rs17543429	1.00[CHB][hapmap]
rs1781740	0.85[CEU][hapmap];0.88[TSI][hapmap]
rs1781742	0.88[CEU][hapmap];0.88[TSI][hapmap]
rs2748156	1.00[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs2748161	0.89[EUR][1000 genomes]
rs2814882	0.89[EUR][1000 genomes]
rs2814887	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814890	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4236061	0.86[EUR][1000 genomes]
rs4254983	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs55869483	1.00[ASN][1000 genomes]
rs56083119	1.00[ASN][1000 genomes]
rs56250767	1.00[ASN][1000 genomes]
rs6458060	0.85[CEU][hapmap]
rs6924443	1.00[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs72853429	0.89[ASN][1000 genomes]
rs7743871	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761154	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7767041	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2748173	GLO1	cis	cerebellum	SCAN
rs2748173	TAF11	cis	cerebellum	SCAN
rs2748173	GLO1	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

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	chr6:38517800-38535000	Weak transcription	Brain Substantia Nigra	brain
10	chr6:38519200-38538800	Weak transcription	Primary T cells from cord blood	blood
11	chr6:38519200-38539400	Weak transcription	Left Ventricle	heart
12	chr6:38519600-38554800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:38521400-38532000	Weak transcription	Primary B cells from cord blood	blood
14	chr6:38522800-38534800	Weak transcription	Fetal Heart	heart
15	chr6:38522800-38535200	Weak transcription	Psoas Muscle	Psoas
16	chr6:38523000-38571600	Weak transcription	HSMMtube	muscle
17	chr6:38523200-38534800	Weak transcription	NHLF	lung
18	chr6:38524000-38537400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:38524000-38539200	Weak transcription	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links