Variant report

Variant	rs3809128
Chromosome Location	chr12:56709919-56709920
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	ZNF143	chr12:56709575-56710474	GM12878	blood:	n/a	chr12:56710138-56710156 chr12:56710202-56710220 chr12:56710145-56710160 chr12:56710187-56710196 chr12:56710138-56710147 chr12:56710209-56710218 chr12:56710140-56710149
2	POLR2A	chr12:56708686-56710726	HepG2	liver:	n/a	n/a
3	ELF1	chr12:56709407-56710342	GM12878	blood:	n/a	chr12:56710096-56710105
4	CTCF	chr12:56709880-56710030	GM12866	blood:	n/a	chr12:56709972-56709981 chr12:56709969-56709987 chr12:56709971-56709992
5	USF1	chr12:56709712-56710290	K562	blood:	n/a	chr12:56709962-56709973
6	ZMIZ1	chr12:56709462-56710228	K562	blood:	n/a	n/a
7	NR3C1	chr12:56709625-56710145	A549	lung:	n/a	chr12:56709873-56709882
8	GABPA	chr12:56709666-56710534	MCF-7	breast:	n/a	n/a
9	CEBPD	chr12:56709709-56710460	K562	blood:	n/a	n/a
10	E2F6	chr12:56709630-56709930	K562	blood:	n/a	n/a
11	YY1	chr12:56709879-56710432	K562	blood:	n/a	n/a
12	ZBTB33	chr12:56709563-56710032	HepG2	liver:	n/a	chr12:56709871-56709886 chr12:56709870-56709879
13	USF1	chr12:56709697-56710272	K562	blood:	n/a	chr12:56709962-56709973
14	TEAD4	chr12:56709596-56710213	K562	blood:	n/a	n/a
15	REST	chr12:56709110-56710376	HL-60	blood:	n/a	chr12:56709416-56709429 chr12:56709821-56709834
16	HEY1	chr12:56709029-56710161	K562	blood:	n/a	n/a
17	ZBTB33	chr12:56709363-56710416	SK-N-SH	brain:	n/a	chr12:56709871-56709886 chr12:56709870-56709879
18	ZNF143	chr12:56709727-56710475	K562	blood:	n/a	chr12:56710138-56710156 chr12:56710202-56710220 chr12:56710145-56710160 chr12:56710187-56710196 chr12:56710138-56710147 chr12:56710209-56710218 chr12:56710140-56710149
19	SP1	chr12:56709406-56710468	A549	lung:	n/a	chr12:56709473-56709487
20	CHD2	chr12:56709352-56710333	HepG2	liver:	n/a	chr12:56709579-56709589
21	CTCF	chr12:56709715-56710194	K562	blood:	n/a	chr12:56709972-56709981 chr12:56709969-56709987 chr12:56709971-56709992
22	CTCF	chr12:56709900-56710050	Caco-2	colon:	n/a	chr12:56709972-56709981 chr12:56709969-56709987 chr12:56709971-56709992
23	PML	chr12:56709561-56710349	GM12878	blood:	n/a	n/a
24	MYC	chr12:56709571-56710438	MCF10A-Er-Src	breast:	n/a	n/a
25	MAX	chr12:56708928-56710466	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr12:56709180-56710342	K562	blood:	n/a	n/a
27	SIX5	chr12:56709352-56710805	A549	lung:	n/a	chr12:56710138-56710147 chr12:56710140-56710149 chr12:56710187-56710196 chr12:56710136-56710150 chr12:56710208-56710222
28	USF1	chr12:56709377-56710453	SK-N-SH	brain:	n/a	chr12:56709962-56709973
29	PML	chr12:56709402-56710265	MCF-7	breast:	n/a	n/a
30	CTBP2	chr12:56709230-56710139	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr12:56708568-56711261	SK-N-MC	brain:	n/a	n/a
32	CEBPB	chr12:56709617-56710392	Hela-S3	cervix:	n/a	chr12:56710228-56710239
33	CTCF	chr12:56709892-56710035	HepG2	liver:	n/a	chr12:56709972-56709981 chr12:56709969-56709987 chr12:56709971-56709992
34	EP300	chr12:56709659-56710255	GM12878	blood:	n/a	n/a
35	CREB1	chr12:56709406-56710494	GM12878	blood:	n/a	n/a
36	ZEB1	chr12:56709442-56710382	GM12878	blood:	n/a	n/a
37	TAF1	chr12:56709417-56710361	K562	blood:	n/a	n/a
38	CTCF	chr12:56709910-56710061	GM10266	blood:	n/a	chr12:56709972-56709981 chr12:56709969-56709987 chr12:56709971-56709992
39	CTCF	chr12:56709840-56709990	GM12865	blood:	n/a	chr12:56709972-56709981 chr12:56709969-56709987
40	ZBTB7A	chr12:56709750-56710131	HepG2	liver:	n/a	n/a
41	USF1	chr12:56709703-56710363	SK-N-SH_RA	brain:	n/a	chr12:56709962-56709973
42	EP300	chr12:56709702-56710290	K562	blood:	n/a	n/a
43	FOXP2	chr12:56709548-56710185	PFSK-1	brain:	n/a	n/a
44	SMC3	chr12:56709592-56710337	Hela-S3	cervix:	n/a	chr12:56709971-56709985 chr12:56709971-56709979
45	SIN3AK20	chr12:56709523-56710047	PANC-1	pancreas:	n/a	n/a
46	POLR2A	chr12:56709355-56710523	HCT-116	colon:	n/a	n/a
47	MAX	chr12:56709472-56710245	K562	blood:	n/a	n/a
48	POLR2A	chr12:56708516-56710469	PFSK-1	brain:	n/a	n/a
49	USF1	chr12:56709486-56710422	ECC-1	luminal epithelium:	n/a	chr12:56709962-56709973
50	ZEB1	chr12:56709887-56710219	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56650654..56653718-chr12:56708513..56712442,3	K562	blood:
2	chr12:56705654..56712950-chr12:56716015..56720160,8	MCF-7	breast:
3	chr12:56709232..56711338-chr12:56847051..56849989,2	MCF-7	breast:
4	chr12:56709258..56711619-chr12:56711666..56713846,2	MCF-7	breast:
5	chr12:56708314..56710826-chr12:56860625..56862676,3	K562	blood:
6	chr12:56707850..56716783-chr12:56721562..56730442,13	MCF-7	breast:
7	chr12:56708282..56711640-chr12:56860573..56864710,5	K562	blood:
8	chr12:56690986..56698275-chr12:56706607..56711958,20	MCF-7	breast:
9	chr12:56615078..56617831-chr12:56708226..56710350,2	MCF-7	breast:
10	chr12:56581557..56584767-chr12:56708519..56710789,3	K562	blood:
11	chr12:56708394..56711484-chr12:56860870..56863906,7	MCF-7	breast:
12	chr12:56708322..56710476-chr12:56739269..56741494,2	MCF-7	breast:
13	chr12:56707486..56713546-chr12:56723426..56730112,22	MCF-7	breast:
14	chr12:56709376..56709962-chr12:56753438..56754246,2	MCF-7	breast:
15	chr12:56708298..56710997-chr12:57029134..57031889,3	MCF-7	breast:
16	chr12:56707342..56711323-chr12:56861186..56863695,3	MCF-7	breast:
17	chr12:56121284..56123165-chr12:56709581..56711185,2	K562	blood:
18	chr12:56659449..56661504-chr12:56708553..56711382,4	K562	blood:
19	chr12:56692256..56696973-chr12:56707335..56712231,9	K562	blood:
20	chr12:56650427..56652210-chr12:56707747..56710356,2	MCF-7	breast:
21	chr12:56708721..56711382-chr12:56864532..56867166,3	K562	blood:
22	chr12:56683725..56686295-chr12:56708413..56711087,2	MCF-7	breast:
23	chr12:56700910..56706653-chr12:56706710..56711113,8	K562	blood:
24	chr12:56707245..56710317-chr12:56714317..56717689,3	MCF-7	breast:
25	chr12:56703600..56706626-chr12:56706710..56710673,5	K562	blood:
26	chr12:56690402..56700610-chr12:56705161..56712229,20	K562	blood:
27	chr12:56708683..56714635-chr12:56725804..56730296,12	K562	blood:
28	chr12:56582213..56584132-chr12:56708371..56710862,2	MCF-7	breast:
29	chr12:56544606..56546956-chr12:56708353..56710252,2	K562	blood:

Variant related genes	Relation type
ENSG00000144785	TF binding region
CNPY2	TF binding region
ENSG00000196465	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000257740	Chromatin interaction
ENSG00000135473	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000170581	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000135423	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000135517	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000176422	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs3816804	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7133285	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	25429064	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3809128	ENSG00000144785	cis	multi-tissue	Pritchard
rs3809128	TMEM4	cis	multi-tissue	Pritchard
rs3809128	CNPY2	cis	lymphoblastoid	seeQTL
rs3809128	RPS26	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56708400-56710400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
2	chr12:56708400-56710800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:56708600-56710000	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr12:56708600-56710600	Active TSS	H1 Cell Line	embryonic stem cell
5	chr12:56708600-56710600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:56708800-56710200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:56708800-56710200	Active TSS	HSMMtube	muscle
8	chr12:56708800-56710400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr12:56708800-56710400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:56708800-56710400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:56708800-56710400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:56708800-56710600	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr12:56708800-56710600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:56708800-56710600	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr12:56708800-56710600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:56708800-56710600	Active TSS	Fetal Kidney	kidney
17	chr12:56708800-56710600	Active TSS	A549	lung
18	chr12:56708800-56710800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:56708800-56710800	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr12:56708800-56710800	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr12:56708800-56710800	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr12:56708800-56710800	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr12:56708800-56710800	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr12:56709000-56710200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:56709000-56710200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:56709000-56710200	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr12:56709000-56710200	Active TSS	Small Intestine	intestine
28	chr12:56709000-56710200	Active TSS	HMEC	breast
29	chr12:56709000-56710400	Active TSS	Aorta	Aorta
30	chr12:56709000-56710400	Active TSS	Brain Cingulate Gyrus	brain
31	chr12:56709000-56710400	Active TSS	Esophagus	oesophagus
32	chr12:56709000-56710400	Active TSS	Fetal Intestine Large	intestine
33	chr12:56709000-56710400	Active TSS	Gastric	stomach
34	chr12:56709000-56710400	Active TSS	Ovary	ovary
35	chr12:56709000-56710400	Active TSS	NHDF-Ad	bronchial
36	chr12:56709000-56710400	Active TSS	NHEK	skin
37	chr12:56709000-56710600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:56709000-56710600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr12:56709000-56710600	Active TSS	H9 Cell Line	embryonic stem cell
40	chr12:56709000-56710600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:56709000-56710600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:56709000-56710600	Active TSS	Fetal Intestine Small	intestine
43	chr12:56709000-56710600	Active TSS	Pancreas	Pancrea
44	chr12:56709000-56710600	Active TSS	HUVEC	blood vessel
45	chr12:56709000-56710600	Active TSS	K562	blood
46	chr12:56709000-56710600	Active TSS	NH-A	brain
47	chr12:56709000-56710600	Active TSS	NHLF	lung
48	chr12:56709000-56710800	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr12:56709000-56710800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:56709000-56710800	Active TSS	GM12878-XiMat	blood

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