Variant report

Variant	rs7634701
Chromosome Location	chr3:119421934-119421935
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	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	POLR2A	chr3:119421928-119421955	MCF-7	breast:	n/a	n/a
16	SIN3AK20	chr3:119421533-119422073	SK-N-SH	brain:	n/a	n/a
17	SP4	chr3:119421579-119422285	H1-hESC	embryonic stem cell:	n/a	n/a
18	ZNF143	chr3:119421391-119422020	H1-hESC	embryonic stem cell:	n/a	chr3:119421538-119421556
19	USF1	chr3:119421707-119422030	SK-N-SH_RA	brain:	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	CHD2	chr3:119421447-119422044	GM12878	blood:	n/a	chr3:119421549-119421559 chr3:119421542-119421552
45	TAF1	chr3:119421797-119422071	H1-hESC	embryonic stem cell:	n/a	n/a
46	ZBTB7A	chr3:119421870-119422396	ECC-1	luminal epithelium:	n/a	chr3:119422299-119422310
47	TCF12	chr3:119421416-119422113	ECC-1	luminal epithelium:	n/a	n/a
48	NR2F2	chr3:119421412-119422087	MCF-7	breast:	n/a	n/a
49	MAX	chr3:119421387-119422207	SK-N-SH	brain:	n/a	n/a
50	YY1	chr3:119421774-119422043	GM12878	blood:	n/a	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
ENSG00000138495	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10934496	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11917710	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13082557	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13092631	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34205825	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34605021	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34845376	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35010368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35012220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35141348	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35228066	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35403027	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35647314	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35864899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35918837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35931410	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4234664	1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4444744	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4544652	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4687877	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4688028	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4688029	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67287047	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6771837	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6778570	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6786722	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6801778	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71325399	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72963166	0.95[AFR][1000 genomes]
rs7612861	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7612954	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7613408	1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7615769	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7617287	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7617290	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7624404	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	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9847068	0.93[CHB][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs9848716	0.93[CHB][hapmap];0.81[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7634701	MAATS1	cis	Thyroid	GTEx
rs7634701	MAATS1	cis	Stomach	GTEx
rs7634701	MAATS1	cis	Artery Tibial	GTEx
rs7634701	MAATS1	cis	Skin Sun Exposed Lower leg	GTEx
rs7634701	C3orf15	cis	multi-tissue	Pritchard

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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