Variant report

Variant	rs162039
Chromosome Location	chr5:7887456-7887457
allele	C/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	STAT3	chr5:7887258-7887560	MCF10A-Er-Src	breast:	n/a	chr5:7887272-7887280
2	CTCF	chr5:7887380-7887530	HAc	cerebellar:	n/a	chr5:7887381-7887402
3	CTCF	chr5:7887181-7887587	K562	blood:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
4	CTCF	chr5:7887139-7887577	GM12878	blood:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
5	RAD21	chr5:7887217-7887576	SK-N-SH_RA	brain:	n/a	chr5:7887380-7887399 chr5:7887382-7887389
6	ZNF143	chr5:7887206-7887583	GM12878	blood:	n/a	n/a
7	CTCF	chr5:7887320-7887470	HBMEC	blood vessel:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
8	CTCF	chr5:7887274-7887487	K562	blood:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
9	CTCF	chr5:7887320-7887470	AG10803	skin:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
10	CTCF	chr5:7887320-7887470	HCPEpiC	choroid plexus:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
11	CTCF	chr5:7887273-7887520	Medullo	brain:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
12	CTCF	chr5:7887320-7887470	HFF-Myc	foreskin:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
13	CTCF	chr5:7887340-7887490	GM06990	blood:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
14	CTCF	chr5:7887320-7887470	Hela-S3	cervix:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
15	CTCF	chr5:7887340-7887490	GM12878	blood:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
16	CTCF	chr5:7887270-7887616	MCF-7	breast:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
17	CTCF	chr5:7887360-7887510	GM12875	blood:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
18	RAD21	chr5:7887118-7887604	IMR90	lung:	n/a	chr5:7887380-7887399 chr5:7887382-7887389
19	CTCF	chr5:7887340-7887490	GM12867	blood:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
20	CTCF	chr5:7887340-7887490	AoAF	blood vessel:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
21	ELF1	chr5:7887198-7887626	A549	lung:	n/a	chr5:7887452-7887463 chr5:7887452-7887463 chr5:7887450-7887463 chr5:7887453-7887462
22	CTCF	chr5:7887320-7887470	AG09309	skin:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
23	CTCF	chr5:7887136-7887466	GM10248	blood:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
24	CTCF	chr5:7887340-7887490	HVMF	connective:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
25	CTCF	chr5:7887320-7887470	GM12871	blood:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
26	RAD21	chr5:7887210-7887574	HepG2	liver:	n/a	chr5:7887380-7887399 chr5:7887382-7887389
27	RAD21	chr5:7887083-7887622	HCT-116	colon:	n/a	chr5:7887380-7887399 chr5:7887382-7887389
28	RAD21	chr5:7887276-7887528	GM12878	blood:	n/a	chr5:7887380-7887399 chr5:7887382-7887389
29	CTCF	chr5:7887340-7887490	BJ	skin:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
30	CTCF	chr5:7887360-7887510	HRE	kidney:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
31	CTCF	chr5:7887360-7887510	HMEC	breast:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
32	CTCF	chr5:7887320-7887470	HMF	breast:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
33	RAD21	chr5:7886902-7887606	SK-N-SH	brain:	n/a	chr5:7887380-7887399 chr5:7887382-7887389
34	RAD21	chr5:7887174-7887620	A549	lung:	n/a	chr5:7887380-7887399 chr5:7887382-7887389
35	CTCF	chr5:7887360-7887510	NHDF-neo	bronchial:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
36	RAD21	chr5:7887115-7887618	A549	lung:	n/a	chr5:7887380-7887399 chr5:7887382-7887389
37	CTCF	chr5:7887350-7887495	MCF-7	breast:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
38	CTCF	chr5:7887360-7887510	K562	blood:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
39	CTCF	chr5:7887235-7887523	Spleen_OC	spleen:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
40	CTCF	chr5:7887340-7887490	GM12872	blood:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
41	ARID3A	chr5:7887185-7887551	HepG2	liver:	n/a	n/a
42	CTCF	chr5:7887340-7887490	HCPEpiC	choroid plexus:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
43	CTCF	chr5:7887320-7887470	AG04450	lung:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
44	CTCF	chr5:7887320-7887470	SK-N-SH_RA	brain:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
45	CTCF	chr5:7887320-7887470	AG04449	skin:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
46	CTCF	chr5:7887274-7887462	HepG2	liver:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
47	RAD21	chr5:7887133-7887603	ECC-1	luminal epithelium:	n/a	chr5:7887380-7887399 chr5:7887382-7887389
48	CTCF	chr5:7887400-7887550	HFF-Myc	foreskin:	n/a	n/a
49	RAD21	chr5:7887227-7887537	SK-N-SH_RA	brain:	n/a	chr5:7887380-7887399 chr5:7887382-7887389
50	CTCF	chr5:7887320-7887470	SAEC	small airway:	n/a	chr5:7887379-7887397 chr5:7887381-7887402

No.	Distal block	Cell Line	Cell type
1	chr5:7867651..7870301-chr5:7886397..7888680,2	MCF-7	breast:
2	chr5:7887367..7887882-chr5:9207640..9208590,2	K562	blood:
3	chr5:7873979..7876833-chr5:7886025..7888380,2	K562	blood:

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

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10063685	0.81[CHB][hapmap]
rs10380	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10520874	0.80[CEU][hapmap];1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs12347	0.95[CEU][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs161870	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs161871	0.81[CEU][hapmap]
rs162026	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs162028	0.86[EUR][1000 genomes]
rs162034	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs162035	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs162036	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	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs162131	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16879305	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16879356	0.99[ASN][1000 genomes]
rs16879410	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs1994867	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2277958	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs227872	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2303081	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2640666	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs326118	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs326125	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326210	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs327581	0.89[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs327583	0.81[ASN][1000 genomes]
rs327586	0.98[ASN][1000 genomes]
rs327592	0.94[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3776454	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4702507	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs56219526	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57085915	0.96[ASN][1000 genomes]
rs57937475	0.96[ASN][1000 genomes]
rs72716547	0.93[ASN][1000 genomes]
rs7727290	0.98[ASN][1000 genomes]
rs9332	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];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	nsv525097	chr5:7887109-7896511	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs162039	MTRR	cis	Lymphoblastoid	GTEx
rs162039	MTRR	Cis_1M	lymphoblastoid	RTeQTL

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	chr5:7871600-7887600	Strong transcription	Placenta	Placenta
9	chr5:7871600-7902800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:7871600-7905000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr5:7871600-7906400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:7871600-7906800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:7871800-7907400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr5:7872000-7895200	Strong transcription	Fetal Muscle Leg	muscle
15	chr5:7873200-7887600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:7873200-7903400	Strong transcription	Dnd41	blood
17	chr5:7873400-7904000	Strong transcription	Hela-S3	cervix
18	chr5:7874000-7890800	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr5:7874000-7905400	Strong transcription	Primary T cells from cord blood	blood
20	chr5:7874000-7909200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:7874600-7894400	Strong transcription	Adipose Nuclei	Adipose
22	chr5:7874800-7887600	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr5:7875000-7906600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:7875400-7895200	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr5:7875400-7903600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr5:7875400-7903800	Strong transcription	Primary B cells from peripheral blood	blood
27	chr5:7875400-7904200	Strong transcription	Primary hematopoietic stem cells	blood
28	chr5:7875400-7904400	Strong transcription	Fetal Muscle Trunk	muscle
29	chr5:7875600-7904400	Strong transcription	Left Ventricle	heart
30	chr5:7878600-7911800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr5:7878800-7888600	Weak transcription	Psoas Muscle	Psoas
32	chr5:7878800-7890600	Strong transcription	NH-A	brain
33	chr5:7879200-7901800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:7879200-7906400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr5:7879400-7889800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr5:7879600-7900600	Strong transcription	Primary B cells from cord blood	blood
37	chr5:7880000-7894400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr5:7880000-7903600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:7880200-7887600	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr5:7880200-7892000	Strong transcription	GM12878-XiMat	blood
41	chr5:7880200-7894200	Weak transcription	Stomach Mucosa	stomach
42	chr5:7880400-7906600	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr5:7880600-7907000	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr5:7880800-7903800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr5:7881000-7904400	Strong transcription	Fetal Intestine Large	intestine
46	chr5:7882200-7902200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr5:7882400-7898600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr5:7882400-7905000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr5:7882600-7898600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr5:7883800-7894400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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