Variant report

Variant	rs8659
Chromosome Location	chr5:7900833-7900834
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:7898057-7905443	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:7867976..7870362-chr5:7899262..7901515,2	K562	blood:
2	chr5:7867721..7870602-chr5:7899852..7901700,2	MCF-7	breast:

Variant related genes	Relation type
MTRR	TF binding region
ENSG00000124279	Chromatin interaction
ENSG00000124275	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10064565	0.94[ASN][1000 genomes]
rs10475399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10520873	0.90[JPT][hapmap]
rs11134265	0.90[CHB][hapmap]
rs12347	0.86[YRI][hapmap]
rs13166314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs161871	0.86[YRI][hapmap]
rs162034	0.81[YRI][hapmap]
rs162035	0.86[YRI][hapmap]
rs162036	0.86[YRI][hapmap]
rs16879418	0.90[JPT][hapmap]
rs3733784	0.89[CHB][hapmap]
rs3776455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3776465	0.85[JPT][hapmap]
rs4277880	0.89[CHB][hapmap]
rs7703033	0.90[JPT][hapmap]
rs9332	0.86[YRI][hapmap]

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	nsv933954	chr5:7897495-7900858	Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs8659	MTRR	Cis_1M	lymphoblastoid	RTeQTL
rs8659	MTRR	cis	Temporal Cortex	GTEx
rs8659	MTRR	cis	multi-tissue	Pritchard
rs8659	MTRR	cis	Cerebellum	GTEx
rs8659	MTRR	cis	Frontal Cortex	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7870200-7903400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:7871200-7903400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:7871200-7903600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr5:7871200-7903800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr5:7871400-7902400	Strong transcription	K562	blood
6	chr5:7871400-7903800	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:7871600-7902800	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:7871600-7905000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr5:7871600-7906400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:7871600-7906800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:7871800-7907400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:7873200-7903400	Strong transcription	Dnd41	blood
13	chr5:7873400-7904000	Strong transcription	Hela-S3	cervix
14	chr5:7874000-7905400	Strong transcription	Primary T cells from cord blood	blood
15	chr5:7874000-7909200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr5:7875000-7906600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:7875400-7903600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:7875400-7903800	Strong transcription	Primary B cells from peripheral blood	blood
19	chr5:7875400-7904200	Strong transcription	Primary hematopoietic stem cells	blood
20	chr5:7875400-7904400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr5:7875600-7904400	Strong transcription	Left Ventricle	heart
22	chr5:7878600-7911800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr5:7879200-7901800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:7879200-7906400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr5:7880000-7903600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:7880400-7906600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr5:7880600-7907000	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr5:7880800-7903800	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr5:7881000-7904400	Strong transcription	Fetal Intestine Large	intestine
30	chr5:7882200-7902200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
31	chr5:7882400-7905000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr5:7885400-7904000	Strong transcription	A549	lung
33	chr5:7885400-7904800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:7887600-7906800	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr5:7888000-7901400	Strong transcription	HSMM	muscle
36	chr5:7888200-7904000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr5:7888200-7904000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:7888200-7904200	Strong transcription	Liver	Liver
39	chr5:7888400-7903000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr5:7888400-7904000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr5:7888400-7904200	Strong transcription	Placenta	Placenta
42	chr5:7888400-7906400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr5:7888600-7901800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr5:7888600-7901800	Strong transcription	NHDF-Ad	bronchial
45	chr5:7888600-7901800	Strong transcription	Osteobl	bone
46	chr5:7888600-7902600	Strong transcription	HMEC	breast
47	chr5:7888600-7903600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr5:7888600-7904000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:7888600-7904200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr5:7888600-7906600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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