Variant report

Variant	rs162036
Chromosome Location	chr5:7885959-7885960
allele	A/G
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	chr5:7884366-7886330	K562	blood:	n/a	n/a
2	POLR2A	chr5:7885866-7886241	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:7866975..7869850-chr5:7885041..7887303,3	K562	blood:
2	chr5:7874190..7876612-chr5:7884831..7887191,2	K562	blood:

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

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10063685	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs10380	0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.81[ASN][1000 genomes]
rs1046014	0.85[MEX][hapmap]
rs10475399	0.86[YRI][hapmap]
rs10520874	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12347	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13166314	0.86[YRI][hapmap]
rs161870	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs161871	1.00[ASW][hapmap];0.81[CEU][hapmap];0.82[LWK][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs162026	0.95[CEU][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs162028	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs162034	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs162035	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs162039	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162041	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs162050	0.82[AFR][1000 genomes]
rs162131	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16879305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16879356	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16879410	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1994867	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2277958	0.99[ASN][1000 genomes]
rs227872	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2303081	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2640666	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs326118	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs326125	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326210	1.00[CEU][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs327581	0.89[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.89[MKK][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs327583	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs327586	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs327592	0.94[CHB][hapmap];0.88[JPT][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3776454	0.81[ASN][1000 genomes]
rs3776455	0.86[YRI][hapmap]
rs4702507	0.82[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs56219526	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57085915	0.96[ASN][1000 genomes]
rs57937475	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72716547	0.93[ASN][1000 genomes]
rs7727290	0.98[ASN][1000 genomes]
rs8659	0.86[YRI][hapmap]
rs9332	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs162036	MTRR	cis	lymphoblastoid	seeQTL
rs162036	MTRR	cis	Lymphoblastoid	GTEx
rs162036	MTRR	Cis_1M	lymphoblastoid	RTeQTL
rs162036	MTRR	cis	multi-tissue	Pritchard
rs162036	MTRR	cis	Liver	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	chr5:7871000-7894000	Weak transcription	Fetal Heart	heart
3	chr5:7871200-7903400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:7871200-7903600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:7871200-7903800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:7871400-7902400	Strong transcription	K562	blood
7	chr5:7871400-7903800	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr5:7871600-7886800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:7871600-7887200	Strong transcription	Fetal Thymus	thymus
10	chr5:7871600-7887600	Strong transcription	Placenta	Placenta
11	chr5:7871600-7902800	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:7871600-7905000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:7871600-7906400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:7871600-7906800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:7871800-7907400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr5:7872000-7886400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr5:7872000-7895200	Strong transcription	Fetal Muscle Leg	muscle
18	chr5:7872800-7887400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:7873200-7887600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:7873200-7903400	Strong transcription	Dnd41	blood
21	chr5:7873400-7904000	Strong transcription	Hela-S3	cervix
22	chr5:7874000-7890800	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:7874000-7905400	Strong transcription	Primary T cells from cord blood	blood
24	chr5:7874000-7909200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr5:7874200-7887000	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr5:7874600-7894400	Strong transcription	Adipose Nuclei	Adipose
27	chr5:7874800-7887400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr5:7874800-7887600	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr5:7875000-7906600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:7875400-7886200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:7875400-7887200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:7875400-7887400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr5:7875400-7895200	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr5:7875400-7903600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr5:7875400-7903800	Strong transcription	Primary B cells from peripheral blood	blood
36	chr5:7875400-7904200	Strong transcription	Primary hematopoietic stem cells	blood
37	chr5:7875400-7904400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr5:7875600-7886200	Strong transcription	Ovary	ovary
39	chr5:7875600-7886200	Strong transcription	Thymus	Thymus
40	chr5:7875600-7886800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:7875600-7887200	Strong transcription	Fetal Brain Female	brain
42	chr5:7875600-7904400	Strong transcription	Left Ventricle	heart
43	chr5:7877600-7886200	Strong transcription	Fetal Stomach	stomach
44	chr5:7878000-7886000	Genic enhancers	Brain Angular Gyrus	brain
45	chr5:7878600-7911800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr5:7878800-7887400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr5:7878800-7888600	Weak transcription	Psoas Muscle	Psoas
48	chr5:7878800-7890600	Strong transcription	NH-A	brain
49	chr5:7879000-7886200	Strong transcription	NHLF	lung
50	chr5:7879000-7887000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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