Variant report

Variant	rs7969338
Chromosome Location	chr12:47740440-47740441
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	CEBPB	chr12:47740367-47740738	A549	lung:	n/a	chr12:47740538-47740549 chr12:47740536-47740549 chr12:47740538-47740547 chr12:47740536-47740547
2	CEBPD	chr12:47740372-47740676	HepG2	liver:	n/a	chr12:47740537-47740548
3	NFIC	chr12:47740343-47740881	HepG2	liver:	n/a	n/a
4	NFIC	chr12:47740350-47740765	HepG2	liver:	n/a	n/a
5	HNF4G	chr12:47740358-47740828	HepG2	liver:	n/a	chr12:47740618-47740633
6	FOXA1	chr12:47740319-47740891	HepG2	liver:	n/a	n/a
7	RCOR1	chr12:47740406-47740844	HepG2	liver:	n/a	n/a
8	MYBL2	chr12:47740327-47740811	HepG2	liver:	n/a	n/a
9	NR2F2	chr12:47740341-47740904	HepG2	liver:	n/a	n/a
10	ZEB1	chr12:47740305-47740849	HepG2	liver:	n/a	n/a
11	CEBPB	chr12:47740274-47740821	MCF-7	breast:	n/a	chr12:47740538-47740549 chr12:47740536-47740549 chr12:47740538-47740547 chr12:47740536-47740547
12	CEBPB	chr12:47740384-47740739	K562	blood:	n/a	chr12:47740538-47740549 chr12:47740536-47740549 chr12:47740538-47740547 chr12:47740536-47740547
13	CEBPB	chr12:47740271-47740809	A549	lung:	n/a	chr12:47740538-47740549 chr12:47740536-47740549 chr12:47740538-47740547 chr12:47740536-47740547
14	HNF4A	chr12:47740375-47740834	HepG2	liver:	n/a	chr12:47740617-47740632
15	HNF4A	chr12:47740398-47740779	HepG2	liver:	n/a	chr12:47740617-47740632
16	ARID3A	chr12:47740384-47740710	HepG2	liver:	n/a	n/a
17	NR3C1	chr12:47740440-47740794	A549	lung:	n/a	n/a
18	MAFK	chr12:47740388-47740889	HepG2	liver:	n/a	chr12:47740669-47740684
19	CEBPB	chr12:47740333-47740823	HepG2	liver:	n/a	chr12:47740538-47740549 chr12:47740536-47740549 chr12:47740538-47740547 chr12:47740536-47740547
20	MBD4	chr12:47740336-47740834	HepG2	liver:	n/a	n/a
21	CEBPB	chr12:47740378-47740694	HepG2	liver:	n/a	chr12:47740538-47740549 chr12:47740536-47740549 chr12:47740538-47740547 chr12:47740536-47740547
22	MYBL2	chr12:47740308-47740911	HepG2	liver:	n/a	n/a
23	EP300	chr12:47740395-47740816	HepG2	liver:	n/a	chr12:47740551-47740561
24	FOXA2	chr12:47740409-47740808	HepG2	liver:	n/a	n/a
25	SP1	chr12:47740290-47740831	HepG2	liver:	n/a	n/a
26	MAFF	chr12:47740387-47740887	HepG2	liver:	n/a	chr12:47740667-47740685
27	RXRA	chr12:47740422-47740795	HepG2	liver:	n/a	n/a
28	CEBPB	chr12:47740292-47740743	HepG2	liver:	n/a	chr12:47740538-47740549 chr12:47740536-47740549 chr12:47740538-47740547 chr12:47740536-47740547
29	TEAD4	chr12:47740282-47741023	HepG2	liver:	n/a	n/a
30	HNF4G	chr12:47740312-47740775	HepG2	liver:	n/a	chr12:47740618-47740633
31	SMC3	chr12:47740438-47740741	HepG2	liver:	n/a	n/a
32	CEBPB	chr12:47740299-47740734	A549	lung:	n/a	chr12:47740538-47740549 chr12:47740536-47740549 chr12:47740538-47740547 chr12:47740536-47740547
33	CEBPB	chr12:47740342-47740815	HepG2	liver:	n/a	chr12:47740538-47740549 chr12:47740536-47740549 chr12:47740538-47740547 chr12:47740536-47740547
34	FOXA2	chr12:47740302-47740837	A549	lung:	n/a	n/a
35	MAFK	chr12:47740402-47740875	HepG2	liver:	n/a	chr12:47740669-47740684
36	HDAC2	chr12:47740380-47740870	HepG2	liver:	n/a	chr12:47740551-47740560
37	FOXA1	chr12:47740394-47740837	HepG2	liver:	n/a	n/a
38	EP300	chr12:47740402-47740723	HepG2	liver:	n/a	chr12:47740551-47740561
39	HNF4A	chr12:47740365-47740812	HepG2	liver:	n/a	chr12:47740617-47740632
40	ZEB1	chr12:47740370-47740942	HepG2	liver:	n/a	n/a
41	FOXA2	chr12:47740433-47740783	A549	lung:	n/a	n/a
42	FOXA1	chr12:47740355-47740769	HepG2	liver:	n/a	n/a
43	EP300	chr12:47740331-47740868	HepG2	liver:	n/a	chr12:47740551-47740561
44	FOXA1	chr12:47740285-47740819	HepG2	liver:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AMIGO2-7	chr12:47740370-47740663	expReg_chr12_3718_-

Variant related genes	Relation type
ENSG00000199566	TF binding region
ENSG00000258116	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10748469	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10785674	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10785676	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10881095	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10881097	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11183899	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11183919	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12302802	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58058166	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6582705	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7956037	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7966682	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7967683	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs886260	0.86[CHB][hapmap];0.92[MEX][hapmap]

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	esv2751100	chr12:47541390-47746157	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv558785	chr12:47740440-48044011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7969338	HDAC7	cis	parietal	SCAN
rs7969338	SLC38A4	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47723200-47742200	Weak transcription	Primary T cells from cord blood	blood
2	chr12:47737400-47748400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:47737600-47741600	Enhancers	Liver	Liver
4	chr12:47740000-47740600	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr12:47740000-47741000	Enhancers	Stomach Mucosa	stomach
6	chr12:47740000-47741000	Enhancers	A549	lung
7	chr12:47740000-47741200	Enhancers	HepG2	liver
8	chr12:47740200-47740800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr12:47740200-47740800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr12:47740200-47740800	Enhancers	Osteobl	bone
11	chr12:47740200-47741000	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr12:47740200-47742400	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr12:47740400-47740800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:47740400-47740800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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