Variant report

Variant	rs12653464
Chromosome Location	chr5:7870095-7870096
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:35)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:35 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr5:7868593-7870261	HEK293-T-REx	kidney:	n/a	n/a
2	POLR2A	chr5:7868367-7870981	K562	blood:	n/a	n/a
3	POLR2A	chr5:7868187-7870260	K562	blood:	n/a	n/a
4	CCNT2	chr5:7868903-7870169	K562	blood:	n/a	n/a
5	STAT3	chr5:7869948-7870214	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr5:7868822-7870098	GM18505	blood:	n/a	n/a
7	WRNIP1	chr5:7869913-7870169	GM12878	blood:	n/a	n/a
8	POLR2A	chr5:7868335-7870230	GM12891	blood:	n/a	n/a
9	MXI1	chr5:7867903-7870446	SK-N-SH	brain:	n/a	n/a
10	HCFC1	chr5:7868144-7871042	Hela-S3	cervix:	n/a	n/a
11	ARID3A	chr5:7869983-7870183	K562	blood:	n/a	n/a
12	SIN3A	chr5:7868545-7870188	H1-hESC	embryonic stem cell:	n/a	chr5:7869683-7869696
13	CHD1	chr5:7868911-7870128	GM12878	blood:	n/a	chr5:7868953-7868963
14	MYC	chr5:7868625-7870342	K562	blood:	n/a	chr5:7868883-7868890
15	MXI1	chr5:7868424-7870235	GM12878	blood:	n/a	n/a
16	SMARCC1	chr5:7868499-7870109	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr5:7868294-7870616	MCF10A-Er-Src	breast:	n/a	n/a
18	SMARCC2	chr5:7868389-7870186	Hela-S3	cervix:	n/a	n/a
19	SIN3A	chr5:7868914-7870136	GM12878	blood:	n/a	chr5:7869683-7869696
20	POLR2A	chr5:7868314-7870583	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr5:7868539-7870208	PBDE	blood:	n/a	n/a
22	POLR2A	chr5:7868837-7870306	IMR90	lung:	n/a	n/a
23	BHLHE40	chr5:7870017-7870361	K562	blood:	n/a	n/a
24	CUX1	chr5:7869875-7870163	K562	blood:	n/a	n/a
25	MAX	chr5:7868188-7870214	NB4	blood:	n/a	chr5:7868883-7868890
26	POLR2A	chr5:7868533-7870202	Raji	blood:	n/a	n/a
27	SIN3AK20	chr5:7868626-7870224	MCF-7	breast:	n/a	n/a
28	MYC	chr5:7868678-7870123	Hela-S3	cervix:	n/a	chr5:7868883-7868890
29	RCOR1	chr5:7868519-7870229	K562	blood:	n/a	n/a
30	RCOR1	chr5:7869966-7870105	K562	blood:	n/a	n/a
31	MXI1	chr5:7868250-7870245	IMR90	lung:	n/a	n/a
32	MXI1	chr5:7869829-7870234	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr5:7868737-7870309	GM18951	blood:	n/a	n/a
34	EP300	chr5:7869811-7870193	K562	blood:	n/a	n/a
35	POLR2A	chr5:7868441-7870118	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:7870060-7870110	GM12878	blood:	n/a
2	chr5:7870060-7870110	Hela-S3	cervix:	n/a
3	chr5:7870060-7870110	SK-N-SH	brain:	n/a
4	chr5:7870060-7870110	AG04449	skin:	fetal
5	chr5:7870060-7870110	NT2-D1	testis:	n/a
6	chr5:7870060-7870110	GM12891	blood:	n/a
7	chr5:7870060-7870110	HRPEpiC	eye:	n/a
8	chr5:7870060-7870110	HEK293	kidney:	embryo
9	chr5:7870060-7870110	HAEpiC	amniotic membrane:	n/a
10	chr5:7870060-7870110	T-47D	breast:	n/a
11	chr5:7870060-7870110	HMEC	breast:	n/a
12	chr5:7870060-7870110	HCF	heart:	n/a
13	chr5:7870060-7870110	HCPEpiC	choroid plexus:	n/a
14	chr5:7870060-7870110	ovcar-3	ovarian:	n/a
15	chr5:7870060-7870110	LNCaP	prostate:	n/a
16	chr5:7870060-7870110	BJ	skin:	n/a
17	chr5:7870060-7870110	GM12892	blood:	n/a
18	chr5:7870060-7870110	MCF-7	breast:	n/a
19	chr5:7870060-7870110	PANC-1	pancreas:	n/a
20	chr5:7870060-7870110	HNPCEpiC	eye:	n/a
21	chr5:7870060-7870110	Caco-2	colon:	n/a
22	chr5:7870060-7870110	NHBE	bronchial:	n/a
23	chr5:7870060-7870110	SK-N-SH_RA	brain:	n/a
24	chr5:7870060-7870110	Hepatocyte	liver:	n/a
25	chr5:7870060-7870110	CMK	blood:	n/a
26	chr5:7870060-7870110	NH-A	brain:	n/a
27	chr5:7870060-7870110	HCM	heart:	n/a
28	chr5:7870060-7870110	U87	brain:	n/a
29	chr5:7870060-7870110	HCT-116	colon:	n/a
30	chr5:7870060-7870110	HUVEC	blood vessel:	n/a
31	chr5:7870060-7870110	ECC-1	luminal epithelium:	n/a
32	chr5:7870060-7870110	IMR90	lung:	fetal
33	chr5:7870060-7870110	PrEC	prostate:	n/a
34	chr5:7870060-7870110	HRE	kidney:	n/a
35	chr5:7870060-7870110	SAEC	small airway:	n/a
36	chr5:7870060-7870110	PFSK-1	brain:	n/a
37	chr5:7870060-7870110	HRCEpiC	kidney:	n/a
38	chr5:7870060-7870110	GM19239	blood:	n/a
39	chr5:7870060-7870110	SKMC	muscle:	n/a
40	chr5:7870060-7870110	H1-hESC	embryonic stem cell:	embryo
41	chr5:7870060-7870110	HL-60	blood:	n/a
42	chr5:7870060-7870110	BE2_C	brain:	n/a
43	chr5:7870060-7870110	Jurkat	blood:	n/a
44	chr5:7870060-7870110	NB4	blood:	n/a
45	chr5:7870060-7870110	AG04450	lung:	fetal
46	chr5:7870060-7870110	RPTEC	kidney:	n/a
47	chr5:7870060-7870110	HEEpiC	esophagus:	n/a
48	chr5:7870060-7870110	AG10803	skin:	n/a
49	chr5:7870060-7870110	HPAEpiC	pulmonary alveolar:	n/a
50	chr5:7870060-7870110	HIPEpiC	eye:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:7867721..7870602-chr5:7899852..7901700,2	MCF-7	breast:
2	chr5:7849253..7853514-chr5:7868734..7871211,5	MCF-7	breast:
3	chr5:7867651..7870301-chr5:7886397..7888680,2	MCF-7	breast:
4	chr5:7867976..7870362-chr5:7899262..7901515,2	K562	blood:

No data

Variant related genes	Relation type
FASTKD3	TF binding region
MTRR	TF binding region
MTRR	CpG island
FASTKD3	CpG island
ENSG00000124275	Chromatin interaction
ENSG00000215217	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11134265	0.85[ASN][1000 genomes]
rs1801394	1.00[ASN][1000 genomes]
rs2307116	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326209	0.90[EUR][1000 genomes]
rs3733784	0.85[ASN][1000 genomes]
rs3776465	0.80[EUR][1000 genomes]
rs3797191	0.81[EUR][1000 genomes]
rs4277880	0.84[ASN][1000 genomes]
rs7703033	0.80[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12653464	MTRR	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7867800-7870400	Active TSS	A549	lung
2	chr5:7867800-7870800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr5:7868000-7870200	Active TSS	GM12878-XiMat	blood
4	chr5:7868000-7870400	Active TSS	Fetal Intestine Large	intestine
5	chr5:7868000-7870400	Active TSS	K562	blood
6	chr5:7868000-7870400	Active TSS	NHDF-Ad	bronchial
7	chr5:7868200-7870200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr5:7868200-7870200	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr5:7868200-7870200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:7868200-7870200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
11	chr5:7868200-7870200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:7868200-7870200	Active TSS	Fetal Muscle Leg	muscle
13	chr5:7868200-7870400	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr5:7868200-7870400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:7868200-7870400	Active TSS	HMEC	breast
16	chr5:7868200-7870400	Active TSS	NHLF	lung
17	chr5:7868200-7870600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:7868200-7870600	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr5:7868200-7870600	Active TSS	Right Atrium	heart
20	chr5:7868200-7870800	Active TSS	H1 Cell Line	embryonic stem cell
21	chr5:7868200-7870800	Active TSS	Psoas Muscle	Psoas
22	chr5:7868200-7870800	Active TSS	Right Ventricle	heart
23	chr5:7868200-7871000	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr5:7868400-7870200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:7868400-7870200	Active TSS	H9 Cell Line	embryonic stem cell
26	chr5:7868400-7870200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr5:7868400-7870200	Active TSS	Aorta	Aorta
28	chr5:7868400-7870200	Active TSS	Esophagus	oesophagus
29	chr5:7868400-7870200	Active TSS	Fetal Muscle Trunk	muscle
30	chr5:7868400-7870200	Active TSS	Placenta	Placenta
31	chr5:7868400-7870200	Active TSS	Gastric	stomach
32	chr5:7868400-7870200	Active TSS	Left Ventricle	heart
33	chr5:7868400-7870200	Active TSS	Lung	lung
34	chr5:7868400-7870200	Active TSS	Pancreas	Pancrea
35	chr5:7868400-7870200	Active TSS	Placenta Amnion	Placenta Amnion
36	chr5:7868400-7870400	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr5:7868400-7870400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr5:7868400-7870400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr5:7868400-7870400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:7868400-7870400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr5:7868400-7870400	Active TSS	Fetal Intestine Small	intestine
42	chr5:7868400-7870400	Active TSS	Ovary	ovary
43	chr5:7868400-7870400	Active TSS	Stomach Mucosa	stomach
44	chr5:7868400-7870400	Active TSS	NHEK	skin
45	chr5:7868400-7870800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:7868400-7870800	Active TSS	Colonic Mucosa	Colon
47	chr5:7868600-7870200	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr5:7868600-7870200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
49	chr5:7868600-7870200	Active TSS	Muscle Satellite Cultured Cells	--
50	chr5:7868600-7870200	Active TSS	Pancreatic Islets	Pancreatic Islet

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