Variant report

Variant	rs17101765
Chromosome Location	chr14:64759869-64759870
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12323665	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17179740	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2978381	0.87[GIH][hapmap]
rs2987983	1.00[CEU][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs3020444	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3020449	0.87[GIH][hapmap]
rs3020450	0.88[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3783736	1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap]
rs6573553	0.87[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs7148637	0.80[MEX][hapmap]
rs7154455	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.80[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8011682	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8020356	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs867443	0.83[CEU][hapmap]
rs960070	0.80[CHB][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1307	chr14:64742037-64787315	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17101765	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs17101765	MTHFD1	cis	cerebellum	SCAN
rs17101765	KCNH5	cis	parietal	SCAN
rs17101765	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs17101765	MTHFD1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64756600-64760200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr14:64758200-64760200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr14:64758200-64761800	Active TSS	Thymus	Thymus
4	chr14:64759000-64760600	Active TSS	Adipose Nuclei	Adipose
5	chr14:64759000-64761600	Active TSS	Ovary	ovary
6	chr14:64759600-64760000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr14:64759600-64761800	Active TSS	K562	blood
8	chr14:64759800-64760000	Enhancers	GM12878-XiMat	blood

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Input of quick search could be:

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

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