Variant report

Variant	rs16879410
Chromosome Location	chr5:7913668-7913669
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:7912479..7915087-chr5:7923737..7926583,2	K562	blood:
2	chr5:7913593..7916151-chr5:7918931..7921579,2	K562	blood:

Variant related genes	Relation type
ENSG00000251168	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10063685	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs10380	0.94[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1046014	0.81[CEU][hapmap]
rs10520874	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12347	0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs161870	0.92[ASN][1000 genomes]
rs162034	0.87[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs162035	0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs162036	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs162039	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs162041	0.94[ASN][1000 genomes]
rs162131	1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.82[ASN][1000 genomes]
rs16879305	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[ASN][1000 genomes]
rs16879356	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1994867	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2277958	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs227872	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2303081	0.94[ASN][1000 genomes]
rs2640666	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs326125	0.95[ASN][1000 genomes]
rs327581	0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs327583	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs327586	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs327592	0.94[CHB][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs3776454	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4702507	0.83[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap]
rs56153354	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56219526	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs57085915	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57652931	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57937475	0.92[ASN][1000 genomes]
rs72716547	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7727290	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9332	0.82[CHB][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916892	chr5:7634377-8158890	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv949492	chr5:7682909-7953909	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv533983	chr5:7701457-8275379	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv597005	chr5:7860404-8093077	Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv427707	chr5:7866234-7966019	Strong transcription Active TSS Genic enhancers Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv508345	chr5:7890892-7933471	Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16879410	MTRR	cis	multi-tissue	Pritchard

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7900000-7914600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:7903600-7916000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:7904400-7915800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr5:7904800-7915400	Weak transcription	Osteobl	bone
5	chr5:7906200-7916400	Weak transcription	NHEK	skin
6	chr5:7908800-7915600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:7909600-7915600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:7909600-7916400	Weak transcription	HSMMtube	muscle
9	chr5:7909800-7917600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr5:7912800-7915600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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