Variant report

Variant	rs2640665
Chromosome Location	chr5:7927952-7927953
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:7868364..7870448-chr5:7925047..7928034,2	MCF-7	breast:
2	chr5:7927628..7928513-chr5:8394887..8395661,2	MCF-7	breast:
3	chr5:7927725..7928301-chr5:8047816..8048769,2	K562	blood:

Variant related genes	Relation type
ENSG00000124275	Chromatin interaction
ENSG00000124279	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs162032	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs162037	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs162038	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs162040	0.84[ASN][1000 genomes]
rs162045	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs162048	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs162051	0.85[ASN][1000 genomes]
rs162130	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs162270	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs162272	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs162273	0.86[EUR][1000 genomes]
rs16879452	0.99[ASN][1000 genomes]
rs1826541	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994866	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2077744	0.85[ASN][1000 genomes]
rs2613663	0.98[ASN][1000 genomes]
rs2613670	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2624228	0.99[ASN][1000 genomes]
rs2624229	0.99[ASN][1000 genomes]
rs2624230	0.99[ASN][1000 genomes]
rs2624231	0.98[ASN][1000 genomes]
rs2624237	0.89[ASN][1000 genomes]
rs2640664	0.99[ASN][1000 genomes]
rs326122	0.92[ASN][1000 genomes]
rs326124	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs326981	0.88[ASN][1000 genomes]
rs327573	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs49672	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv4706	chr5:7917701-7956246	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2640665	MTRR	Cis_1M	lymphoblastoid	RTeQTL
rs2640665	MTRR	cis	multi-tissue	Pritchard

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7925400-7928000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:7925400-7928200	Enhancers	NHDF-Ad	bronchial
3	chr5:7925400-7928400	Enhancers	Osteobl	bone
4	chr5:7925600-7928000	Enhancers	NH-A	brain
5	chr5:7925800-7928000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr5:7926200-7928000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:7926400-7928000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:7926400-7928400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:7927000-7928200	Weak transcription	Fetal Intestine Small	intestine
10	chr5:7927200-7928200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:7927600-7928000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:7927600-7928400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:7927800-7928000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
14	chr5:7927800-7928000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:7927800-7928000	Enhancers	Liver	Liver
16	chr5:7927800-7928200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr5:7927800-7928400	Enhancers	Fetal Muscle Trunk	muscle
18	chr5:7927800-7928400	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr5:7927800-7929200	Enhancers	Fetal Intestine Large	intestine

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