Variant report

Variant	rs7624404
Chromosome Location	chr3:119421911-119421912
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	MYC	chr3:119421867-119421983	MCF-7	breast:	n/a	n/a
2	SP1	chr3:119421184-119422129	H1-hESC	embryonic stem cell:	n/a	chr3:119421531-119421545 chr3:119421549-119421558 chr3:119421539-119421553 chr3:119421544-119421558 chr3:119421548-119421557 chr3:119421543-119421553 chr3:119421543-119421552 chr3:119421542-119421554 chr3:119421549-119421558 chr3:119421544-119421553 chr3:119421655-119421669 chr3:119421547-119421559 chr3:119421542-119421554
3	MAX	chr3:119421532-119422339	ECC-1	luminal epithelium:	n/a	n/a
4	MAX	chr3:119421635-119422292	A549	lung:	n/a	n/a
5	RUNX3	chr3:119421562-119422102	GM12878	blood:	n/a	n/a
6	MXI1	chr3:119421136-119423363	SK-N-SH	brain:	n/a	n/a
7	MAX	chr3:119421561-119422389	ECC-1	luminal epithelium:	n/a	n/a
8	SIN3AK20	chr3:119421618-119422087	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr3:119421852-119422207	MCF-7	breast:	n/a	n/a
10	MAX	chr3:119421796-119422116	GM12878	blood:	n/a	n/a
11	MYC	chr3:119421454-119422009	H1-hESC	embryonic stem cell:	n/a	n/a
12	JUND	chr3:119421343-119422149	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:119421671-119422068	H1-hESC	embryonic stem cell:	n/a	n/a
14	EP300	chr3:119421909-119421962	GM12878	blood:	n/a	n/a
15	SIN3AK20	chr3:119421533-119422073	SK-N-SH	brain:	n/a	n/a
16	SP4	chr3:119421579-119422285	H1-hESC	embryonic stem cell:	n/a	n/a
17	ZNF143	chr3:119421391-119422020	H1-hESC	embryonic stem cell:	n/a	chr3:119421538-119421556
18	USF1	chr3:119421707-119422030	SK-N-SH_RA	brain:	n/a	n/a
19	SPI1	chr3:119421582-119421916	GM12878	blood:	n/a	n/a
20	MAX	chr3:119421544-119422370	A549	lung:	n/a	n/a
21	POLR2A	chr3:119421413-119422002	U87	brain:	n/a	n/a
22	EP300	chr3:119421458-119421973	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr3:119421402-119422053	SK-N-SH	brain:	n/a	n/a
24	MAX	chr3:119421571-119422280	MCF-7	breast:	n/a	n/a
25	SIN3A	chr3:119421460-119422472	H1-hESC	embryonic stem cell:	n/a	chr3:119422198-119422208 chr3:119422137-119422150
26	MAZ	chr3:119421350-119422533	IMR90	lung:	n/a	n/a
27	YY1	chr3:119421509-119422188	H1-hESC	embryonic stem cell:	n/a	n/a
28	E2F6	chr3:119421665-119422408	H1-hESC	embryonic stem cell:	n/a	chr3:119422278-119422285
29	POLR2A	chr3:119421830-119422063	H1-hESC	embryonic stem cell:	n/a	n/a
30	CHD2	chr3:119421455-119422185	H1-hESC	embryonic stem cell:	n/a	chr3:119421549-119421559 chr3:119421542-119421552
31	SP1	chr3:119421482-119422077	A549	lung:	n/a	chr3:119421531-119421545 chr3:119421549-119421558 chr3:119421539-119421553 chr3:119421544-119421558 chr3:119421548-119421557 chr3:119421543-119421553 chr3:119421543-119421552 chr3:119421542-119421554 chr3:119421549-119421558 chr3:119421544-119421553 chr3:119421655-119421669 chr3:119421547-119421559 chr3:119421542-119421554
32	JUND	chr3:119421579-119421941	H1-hESC	embryonic stem cell:	n/a	n/a
33	MAX	chr3:119421589-119422309	H1-hESC	embryonic stem cell:	n/a	n/a
34	MXI1	chr3:119421753-119422047	GM12878	blood:	n/a	n/a
35	RUNX3	chr3:119421683-119422100	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:119421461-119422143	ECC-1	luminal epithelium:	n/a	n/a
37	MAX	chr3:119421605-119422332	SK-N-SH	brain:	n/a	n/a
38	RAD21	chr3:119421475-119422045	H1-hESC	embryonic stem cell:	n/a	chr3:119421539-119421549
39	RCOR1	chr3:119421744-119421935	GM12878	blood:	n/a	n/a
40	E2F6	chr3:119421652-119422307	H1-hESC	embryonic stem cell:	n/a	chr3:119422278-119422285
41	E2F6	chr3:119421687-119422287	A549	lung:	n/a	chr3:119422278-119422285
42	SP1	chr3:119421545-119422008	GM12878	blood:	n/a	chr3:119421549-119421558 chr3:119421548-119421557 chr3:119421549-119421558 chr3:119421655-119421669 chr3:119421547-119421559
43	RAD21	chr3:119421499-119422057	SK-N-SH_RA	brain:	n/a	chr3:119421539-119421549
44	RELA	chr3:119421346-119421927	GM18951	blood:	n/a	n/a
45	CHD2	chr3:119421447-119422044	GM12878	blood:	n/a	chr3:119421549-119421559 chr3:119421542-119421552
46	TAF1	chr3:119421797-119422071	H1-hESC	embryonic stem cell:	n/a	n/a
47	BHLHE40	chr3:119421891-119421929	GM12878	blood:	n/a	n/a
48	ZBTB7A	chr3:119421870-119422396	ECC-1	luminal epithelium:	n/a	chr3:119422299-119422310
49	TCF12	chr3:119421416-119422113	ECC-1	luminal epithelium:	n/a	n/a
50	NR2F2	chr3:119421412-119422087	MCF-7	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:119421868-119421918	NHDF-neo	bronchial:	n/a
2	chr3:119421868-119421918	SK-N-SH_RA	brain:	n/a
3	chr3:119421868-119421918	PrEC	prostate:	n/a
4	chr3:119421868-119421918	AG09319	gingival:	n/a
5	chr3:119421868-119421918	AG04449	skin:	fetal
6	chr3:119421868-119421918	HCT-116	colon:	n/a
7	chr3:119421868-119421918	GM06990	blood:	n/a
8	chr3:119421868-119421918	BJ	skin:	n/a
9	chr3:119421868-119421918	SKMC	muscle:	n/a
10	chr3:119421868-119421918	HPAEpiC	pulmonary alveolar:	n/a
11	chr3:119421868-119421918	AG10803	skin:	n/a
12	chr3:119421868-119421918	MCF10A-Er-Src	breast:	n/a
13	chr3:119421868-119421918	Hela-S3	cervix:	n/a
14	chr3:119421868-119421918	U87	brain:	n/a
15	chr3:119421868-119421918	GM12891	blood:	n/a
16	chr3:119421868-119421918	AoSMC	blood vessel:	n/a
17	chr3:119421868-119421918	RPTEC	kidney:	n/a
18	chr3:119421868-119421918	IMR90	lung:	fetal
19	chr3:119421868-119421918	HRPEpiC	eye:	n/a
20	chr3:119421868-119421918	HCM	heart:	n/a
21	chr3:119421868-119421918	AG09309	skin:	n/a
22	chr3:119421868-119421918	T-47D	breast:	n/a
23	chr3:119421868-119421918	SK-N-SH	brain:	n/a
24	chr3:119421868-119421918	GM12892	blood:	n/a
25	chr3:119421868-119421918	ProgFib	skin:	n/a
26	chr3:119421868-119421918	BE2_C	brain:	n/a
27	chr3:119421868-119421918	Jurkat	blood:	n/a
28	chr3:119421868-119421918	PFSK-1	brain:	n/a
29	chr3:119421868-119421918	SK-N-MC	brain:	n/a
30	chr3:119421868-119421918	Caco-2	colon:	n/a
31	chr3:119421868-119421918	HCPEpiC	choroid plexus:	n/a
32	chr3:119421868-119421918	CMK	blood:	n/a
33	chr3:119421868-119421918	HMEC	breast:	n/a
34	chr3:119421868-119421918	SAEC	small airway:	n/a
35	chr3:119421868-119421918	AG04450	lung:	fetal
36	chr3:119421868-119421918	HRCEpiC	kidney:	n/a
37	chr3:119421868-119421918	LNCaP	prostate:	n/a
38	chr3:119421868-119421918	HUVEC	blood vessel:	n/a
39	chr3:119421868-119421918	HEEpiC	esophagus:	n/a
40	chr3:119421868-119421918	ovcar-3	ovarian:	n/a
41	chr3:119421868-119421918	MCF-7	breast:	n/a
42	chr3:119421868-119421918	K562	blood:	n/a
43	chr3:119421868-119421918	A549	lung:	n/a
44	chr3:119421868-119421918	HepG2	liver:	n/a
45	chr3:119421868-119421918	Hepatocyte	liver:	n/a
46	chr3:119421868-119421918	NHBE	bronchial:	n/a
47	chr3:119421868-119421918	HRE	kidney:	n/a
48	chr3:119421868-119421918	HAEpiC	amniotic membrane:	n/a
49	chr3:119421868-119421918	GM12878	blood:	n/a
50	chr3:119421868-119421918	HIPEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119393569..119396281-chr3:119421855..119424087,2	MCF-7	breast:

Variant related genes	Relation type
MAATS1	TF binding region
MAATS1	CpG island
ENSG00000138495	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10934496	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11917710	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13082557	0.89[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13092631	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34205825	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34605021	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34845376	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35010368	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35012220	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35141348	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35228066	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35403027	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35647314	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35864899	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35918837	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35931410	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4234664	0.90[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4444744	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4544652	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4687877	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4688028	0.81[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4688029	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67287047	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6771837	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6778570	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6786722	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6801778	0.90[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71325399	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7612861	0.89[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7612954	0.89[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7613408	0.90[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7615769	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7617287	0.89[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7617290	0.89[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7634701	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644545	0.89[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9847068	0.90[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs9848716	0.90[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460834	chr3:119384163-119458851	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv591390	chr3:119384163-119458851	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv591391	chr3:119403145-119442572	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer 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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7624404	MAATS1	cis	Thyroid	GTEx
rs7624404	MAATS1	cis	Artery Tibial	GTEx
rs7624404	MAATS1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119418400-119422200	ZNF genes & repeats	GM12878-XiMat	blood
2	chr3:119421200-119422000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:119421200-119422000	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr3:119421200-119422000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:119421200-119422000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:119421200-119422000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:119421200-119422000	Active TSS	Muscle Satellite Cultured Cells	--
8	chr3:119421200-119422000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:119421200-119422000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:119421200-119422000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:119421200-119422000	Active TSS	Aorta	Aorta
12	chr3:119421200-119422000	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr3:119421200-119422000	Active TSS	Right Ventricle	heart
14	chr3:119421200-119422200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr3:119421200-119422200	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr3:119421200-119422200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr3:119421200-119422200	Active TSS	Brain Substantia Nigra	brain
18	chr3:119421200-119422200	Active TSS	Rectal Smooth Muscle	rectum
19	chr3:119421200-119422200	Flanking Active TSS	A549	lung
20	chr3:119421200-119422200	Active TSS	NHDF-Ad	bronchial
21	chr3:119421200-119422400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr3:119421200-119422400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:119421200-119422400	Active TSS	Brain Angular Gyrus	brain
24	chr3:119421200-119422400	Active TSS	Colon Smooth Muscle	Colon
25	chr3:119421200-119422400	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr3:119421200-119422600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:119421200-119422600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:119421200-119422600	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr3:119421200-119422600	Enhancers	Fetal Heart	heart
30	chr3:119421200-119422600	Active TSS	Fetal Lung	lung
31	chr3:119421200-119422600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr3:119421200-119423200	Active TSS	Brain Anterior Caudate	brain
33	chr3:119421200-119423400	Active TSS	Ovary	ovary
34	chr3:119421400-119422000	Active TSS	H1 Cell Line	embryonic stem cell
35	chr3:119421400-119422000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:119421400-119422000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:119421400-119422000	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr3:119421400-119422000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:119421400-119422000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:119421400-119422000	Active TSS	Fetal Intestine Small	intestine
41	chr3:119421400-119422000	Active TSS	Right Atrium	heart
42	chr3:119421400-119422000	Active TSS	NHLF	lung
43	chr3:119421400-119422200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:119421400-119422200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:119421400-119422200	Flanking Active TSS	Placenta	Placenta
46	chr3:119421400-119422200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
47	chr3:119421400-119422200	Active TSS	Gastric	stomach
48	chr3:119421400-119422400	Active TSS	H9 Cell Line	embryonic stem cell
49	chr3:119421400-119422400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:119421400-119422400	Flanking Active TSS	Primary B cells from peripheral blood	blood

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