Variant report

Variant	rs249209
Chromosome Location	chr5:79867209-79867210
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs118526	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11951910	1.00[JPT][hapmap]
rs1232027	1.00[JPT][hapmap]
rs13161245	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs1382539	0.82[CHD][hapmap]
rs1382540	0.82[CHD][hapmap]
rs1382543	0.82[CHD][hapmap]
rs1478834	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs1643638	1.00[JPT][hapmap]
rs1643649	1.00[JPT][hapmap]
rs1643650	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs1643657	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs1643658	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs1643659	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs1650653	0.82[CHD][hapmap]
rs1650654	0.82[CHD][hapmap]
rs1650665	0.82[CHD][hapmap]
rs1650709	1.00[JPT][hapmap]
rs1677626	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs1677636	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs1677691	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs1677692	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs1677693	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs1677694	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs1677703	0.82[CHD][hapmap]
rs1824837	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs249204	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs249208	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs249218	0.81[EUR][1000 genomes]
rs249219	0.80[EUR][1000 genomes]
rs2560424	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2618372	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2897262	0.82[CHD][hapmap]
rs6151619	1.00[JPT][hapmap]
rs836818	1.00[JPT][hapmap]
rs836821	1.00[JPT][hapmap]
rs836822	1.00[JPT][hapmap]
rs836823	1.00[JPT][hapmap]
rs844370	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs863215	0.90[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027183	chr5:79837249-79876229	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1021286	chr5:79844255-79876229	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1025796	chr5:79844255-79880441	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1034832	chr5:79844255-79892075	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1034384	chr5:79846926-79876229	Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1021853	chr5:79847376-79876229	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1027663	chr5:79855710-79876229	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1020051	chr5:79855710-79879770	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1029820	chr5:79855710-79880441	Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1035021	chr5:79855710-79892075	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1022154	chr5:79855710-79897516	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs249209	ANKRD34B	cis	Whole Blood	GTEx
rs249209	DHFR	cis	Whole Blood	GTEx
rs249209	DHFR	cis	Muscle Skeletal	GTEx
rs249209	HSS00169533	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79867200-79867400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin

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