Variant report

Variant	rs249219
Chromosome Location	chr5:79858271-79858272
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10073069	0.96[ASN][1000 genomes]
rs118526	0.82[EUR][1000 genomes]
rs17263175	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs185105	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2081854	0.81[ASN][1000 genomes]
rs2431218	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs249204	0.82[EUR][1000 genomes]
rs249208	0.80[EUR][1000 genomes]
rs249209	0.80[EUR][1000 genomes]
rs249218	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4563603	1.00[JPT][hapmap]
rs6453521	1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs249219	MSH3	cis	parietal	SCAN
rs249219	ANKRD34B	cis	Whole Blood	GTEx
rs249219	DHFR	cis	Whole Blood	GTEx
rs249219	MSH3	cis	cerebellum	SCAN
rs249219	DP58	cis	multi-tissue	Pritchard
rs249219	DHFR	cis	brain	BrainEAC
rs249219	DHFR	cis	Muscle Skeletal	GTEx
rs249219	RASGRF2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79857200-79858600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:79857400-79858400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
3	chr5:79857400-79858400	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr5:79857600-79858400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
5	chr5:79857600-79858400	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr5:79857800-79858600	Enhancers	H1 Cell Line	embryonic stem cell
7	chr5:79858000-79858400	Enhancers	H9 Cell Line	embryonic stem cell
8	chr5:79858000-79858400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr5:79858000-79858600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
10	chr5:79858000-79858800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:79858200-79858400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:79858200-79858400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	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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