Variant report

Variant	rs2748172
Chromosome Location	chr6:38530300-38530301
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10807196	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10807198	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs10947740	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs10947752	0.89[EUR][1000 genomes]
rs1321056	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1699001	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1699002	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs1699003	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1699005	0.85[EUR][1000 genomes]
rs1699007	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1699017	0.87[EUR][1000 genomes]
rs1739621	0.81[EUR][1000 genomes]
rs1739626	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs1739627	0.96[CEU][hapmap]
rs1739628	0.86[EUR][1000 genomes]
rs1739629	0.86[EUR][1000 genomes]
rs1739630	0.82[EUR][1000 genomes]
rs1739632	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1781708	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1781711	0.85[EUR][1000 genomes]
rs1852979	0.89[EUR][1000 genomes]
rs2092797	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2144328	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2180104	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2252550	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2748164	0.86[ASN][1000 genomes]
rs2748165	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2814883	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2814885	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2814889	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2814894	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4392718	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55949948	0.86[ASN][1000 genomes]
rs6458059	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs6923737	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs6931131	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6932235	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs910516	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs9394508	0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9394521	0.81[EUR][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

No data

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

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