Variant report

Variant	rs1126639
Chromosome Location	chr14:25101548-25101549
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10873219	0.80[GIH][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap];0.85[EUR][1000 genomes]
rs10909625	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];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11539752	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236337	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2236338	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2273844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs45442494	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs45562442	0.81[ASN][1000 genomes]
rs45628336	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6573910	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6573911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8192917	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8192921	0.86[EUR][1000 genomes]
rs9671454	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv510631	chr14:25045183-25172311	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv901502	chr14:25074711-25101706	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1843155	chr14:25099980-25110067	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1126639	SDR39U1	cis	cerebellum	SCAN
rs1126639	SDR39U1	cis	lung	GTEx
rs1126639	CTSG	cis	multi-tissue	Pritchard
rs1126639	RNASE8	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25099400-25102200	Enhancers	Fetal Intestine Small	intestine
2	chr14:25099800-25102000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr14:25100200-25102600	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
4	chr14:25100600-25101600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr14:25100600-25101800	Weak transcription	Fetal Intestine Large	intestine
6	chr14:25100800-25101800	Weak transcription	Fetal Muscle Leg	muscle
7	chr14:25100800-25101800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr14:25100800-25102000	Active TSS	Primary T cells fromperipheralblood	blood
9	chr14:25100800-25109600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr14:25101000-25101800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr14:25101200-25103600	Enhancers	Fetal Thymus	thymus
12	chr14:25101200-25112800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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