Variant report

Variant	rs10520874
Chromosome Location	chr5:7899909-7899910
allele	C/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	chr5:7898057-7905443	K562	blood:	n/a	n/a
2	POLR2A	chr5:7898549-7900055	K562	blood:	n/a	n/a
3	POLR2A	chr5:7899234-7900079	HepG2	liver:	n/a	n/a
4	POLR2A	chr5:7899637-7899914	GM12878	blood:	n/a	n/a
5	POLR2A	chr5:7898485-7900072	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:7867976..7870362-chr5:7899262..7901515,2	K562	blood:
2	chr5:7867721..7870602-chr5:7899852..7901700,2	MCF-7	breast:
3	chr5:7897897..7900344-chr5:7900899..7905029,3	MCF-7	breast:

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

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10063685	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs10380	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1046014	0.94[CEU][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12347	1.00[JPT][hapmap]
rs161870	0.93[ASN][1000 genomes]
rs162034	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs162035	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs162036	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs162039	0.80[CEU][hapmap];1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs162041	0.95[ASN][1000 genomes]
rs162131	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs16879305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16879356	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16879410	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]
rs1994867	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2277958	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227872	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2303079	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs2303081	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2640666	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs326125	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs326210	0.80[CEU][hapmap]
rs327581	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs327586	0.99[ASN][1000 genomes]
rs327592	0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3776454	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41282639	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4702507	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs56153354	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs56219526	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57085915	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57652931	0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs57937475	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61536869	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72716534	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72716536	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72716547	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7727290	0.80[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9332	0.82[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10520874	MTRR	Cis_1M	lymphoblastoid	RTeQTL
rs10520874	MTRR	cis	Lymphoblastoid	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	chr5:7879600-7900600	Strong transcription	Primary B cells from cord blood	blood
26	chr5:7880000-7903600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:7880400-7906600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr5:7880600-7907000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr5:7880800-7903800	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr5:7881000-7904400	Strong transcription	Fetal Intestine Large	intestine
31	chr5:7882200-7902200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
32	chr5:7882400-7905000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr5:7885400-7904000	Strong transcription	A549	lung
34	chr5:7885400-7904800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:7887600-7906800	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr5:7888000-7901400	Strong transcription	HSMM	muscle
37	chr5:7888200-7904000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:7888200-7904000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr5:7888200-7904200	Strong transcription	Liver	Liver
40	chr5:7888400-7903000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr5:7888400-7904000	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr5:7888400-7904200	Strong transcription	Placenta	Placenta
43	chr5:7888400-7906400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:7888600-7900600	Strong transcription	Stomach Smooth Muscle	stomach
45	chr5:7888600-7900600	Strong transcription	HepG2	liver
46	chr5:7888600-7900800	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr5:7888600-7901800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:7888600-7901800	Strong transcription	NHDF-Ad	bronchial
49	chr5:7888600-7901800	Strong transcription	Osteobl	bone
50	chr5:7888600-7902600	Strong transcription	HMEC	breast

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