Variant report

Variant	rs7612954
Chromosome Location	chr3:119422106-119422107
allele	A/C
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	CTCF	chr3:119422060-119422210	SK-N-SH_RA	brain:	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	MXI1	chr3:119421136-119423363	SK-N-SH	brain:	n/a	n/a
6	MAX	chr3:119421561-119422389	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr3:119421852-119422207	MCF-7	breast:	n/a	n/a
8	MAX	chr3:119421796-119422116	GM12878	blood:	n/a	n/a
9	JUND	chr3:119421343-119422149	H1-hESC	embryonic stem cell:	n/a	n/a
10	SP4	chr3:119421579-119422285	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr3:119421544-119422370	A549	lung:	n/a	n/a
12	MAX	chr3:119421571-119422280	MCF-7	breast:	n/a	n/a
13	SIN3A	chr3:119421460-119422472	H1-hESC	embryonic stem cell:	n/a	chr3:119422198-119422208 chr3:119422137-119422150
14	MAZ	chr3:119421350-119422533	IMR90	lung:	n/a	n/a
15	YY1	chr3:119421509-119422188	H1-hESC	embryonic stem cell:	n/a	n/a
16	E2F6	chr3:119421665-119422408	H1-hESC	embryonic stem cell:	n/a	chr3:119422278-119422285
17	CHD2	chr3:119421455-119422185	H1-hESC	embryonic stem cell:	n/a	chr3:119421549-119421559 chr3:119421542-119421552
18	MAX	chr3:119421589-119422309	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr3:119422080-119422230	HBMEC	blood vessel:	n/a	n/a
20	POLR2A	chr3:119421461-119422143	ECC-1	luminal epithelium:	n/a	n/a
21	MAX	chr3:119421605-119422332	SK-N-SH	brain:	n/a	n/a
22	E2F6	chr3:119421652-119422307	H1-hESC	embryonic stem cell:	n/a	chr3:119422278-119422285
23	E2F6	chr3:119421687-119422287	A549	lung:	n/a	chr3:119422278-119422285
24	ZBTB7A	chr3:119421870-119422396	ECC-1	luminal epithelium:	n/a	chr3:119422299-119422310
25	TCF12	chr3:119421416-119422113	ECC-1	luminal epithelium:	n/a	n/a
26	MAX	chr3:119421387-119422207	SK-N-SH	brain:	n/a	n/a
27	MYC	chr3:119421798-119422224	MCF-7	breast:	n/a	n/a
28	REST	chr3:119421254-119422386	H1-neurons	neurons:	n/a	chr3:119422137-119422150 chr3:119422199-119422208
29	MAX	chr3:119421256-119422379	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr3:119421522-119422211	H1-neurons	neurons:	n/a	n/a
31	E2F6	chr3:119421713-119422180	A549	lung:	n/a	n/a
32	SIN3AK20	chr3:119421543-119422225	H1-hESC	embryonic stem cell:	n/a	n/a
33	YY1	chr3:119421513-119422179	SK-N-SH_RA	brain:	n/a	n/a
34	HA-E2F1	chr3:119421551-119422283	MCF-7	breast:	n/a	n/a
35	MAX	chr3:119421753-119422132	A549	lung:	n/a	n/a
36	MAX	chr3:119421543-119422129	H1-hESC	embryonic stem cell:	n/a	n/a
37	MXI1	chr3:119421213-119422295	IMR90	lung:	n/a	n/a
38	MXI1	chr3:119421751-119422191	H1-hESC	embryonic stem cell:	n/a	n/a
39	YY1	chr3:119421461-119422114	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAX	chr3:119421588-119422245	MCF-7	breast:	n/a	n/a
41	ELF1	chr3:119421603-119422375	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: 7 )

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

rs_ID	r²[population]
rs10934496	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11917710	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13082557	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13092631	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34205825	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34605021	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34845376	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35010368	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35012220	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35141348	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35228066	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35403027	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35647314	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35864899	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35918837	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35931410	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4234664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4444744	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4544652	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687877	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4688028	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4688029	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67287047	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6771837	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6778570	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6786722	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6801778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71325399	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72963166	0.95[AFR][1000 genomes]
rs7612861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613408	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7615769	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7617287	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617290	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624404	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]
rs7634701	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]
rs7644545	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9847068	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9848716	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7612954	COX17	cis	lymphoblastoid	seeQTL
rs7612954	MAATS1	cis	Artery Tibial	GTEx
rs7612954	MAATS1	cis	Thyroid	GTEx
rs7612954	C3orf15	cis	lymphoblastoid	seeQTL
rs7612954	MAATS1	cis	Stomach	GTEx
rs7612954	MAATS1	cis	Skin Sun Exposed Lower leg	GTEx
rs7612954	C3orf15	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 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	chr3:119421200-119422200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr3:119421200-119422200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr3:119421200-119422200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
5	chr3:119421200-119422200	Active TSS	Brain Substantia Nigra	brain
6	chr3:119421200-119422200	Active TSS	Rectal Smooth Muscle	rectum
7	chr3:119421200-119422200	Flanking Active TSS	A549	lung
8	chr3:119421200-119422200	Active TSS	NHDF-Ad	bronchial
9	chr3:119421200-119422400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr3:119421200-119422400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:119421200-119422400	Active TSS	Brain Angular Gyrus	brain
12	chr3:119421200-119422400	Active TSS	Colon Smooth Muscle	Colon
13	chr3:119421200-119422400	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr3:119421200-119422600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:119421200-119422600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:119421200-119422600	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr3:119421200-119422600	Enhancers	Fetal Heart	heart
18	chr3:119421200-119422600	Active TSS	Fetal Lung	lung
19	chr3:119421200-119422600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr3:119421200-119423200	Active TSS	Brain Anterior Caudate	brain
21	chr3:119421200-119423400	Active TSS	Ovary	ovary
22	chr3:119421400-119422200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:119421400-119422200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:119421400-119422200	Flanking Active TSS	Placenta	Placenta
25	chr3:119421400-119422200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
26	chr3:119421400-119422200	Active TSS	Gastric	stomach
27	chr3:119421400-119422400	Active TSS	H9 Cell Line	embryonic stem cell
28	chr3:119421400-119422400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:119421400-119422400	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr3:119421400-119422400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
31	chr3:119421400-119422400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr3:119421400-119422400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:119421400-119422400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr3:119421400-119422400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:119421400-119422400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
36	chr3:119421400-119422400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
37	chr3:119421400-119422400	Active TSS	HSMM	muscle
38	chr3:119421400-119422600	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr3:119421400-119422600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
40	chr3:119421400-119422600	Active TSS	Colonic Mucosa	Colon
41	chr3:119421400-119422600	Active TSS	Pancreas	Pancrea
42	chr3:119421400-119423000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:119421400-119423000	Active TSS	Fetal Kidney	kidney
44	chr3:119421400-119423200	Flanking Active TSS	Liver	Liver
45	chr3:119421400-119423200	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr3:119421600-119422200	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr3:119421600-119422200	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr3:119421600-119422200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:119421600-119422200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:119421600-119422200	Active TSS	Placenta Amnion	Placenta Amnion

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