Variant report

Variant	rs12100048
Chromosome Location	chr13:50657362-50657363
allele	G/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	MAZ	chr13:50655566-50657451	IMR90	lung:	n/a	chr13:50656289-50656299 chr13:50656286-50656296
2	CEBPB	chr13:50656093-50657398	Hela-S3	cervix:	n/a	chr13:50657130-50657141 chr13:50657131-50657140 chr13:50657129-50657142
3	GATA1	chr13:50655794-50657455	PBDE	blood:	n/a	n/a
4	TEAD4	chr13:50657069-50657442	K562	blood:	n/a	n/a
5	MAX	chr13:50655553-50657415	HCT-116	colon:	n/a	chr13:50656304-50656314 chr13:50656289-50656299 chr13:50656286-50656296
6	TAL1	chr13:50656416-50657428	K562	blood:	n/a	n/a
7	MAX	chr13:50655028-50657418	A549	lung:	n/a	chr13:50656304-50656314 chr13:50656289-50656299 chr13:50656286-50656296
8	ZNF384	chr13:50656061-50657470	K562	blood:	n/a	n/a
9	CEBPB	chr13:50656919-50657413	MCF-7	breast:	n/a	chr13:50657130-50657141 chr13:50657131-50657140 chr13:50657129-50657142
10	CEBPB	chr13:50656883-50657422	ECC-1	luminal epithelium:	n/a	chr13:50657130-50657141 chr13:50657131-50657140 chr13:50657129-50657142
11	POLR2A	chr13:50654993-50657515	HL-60	blood:	n/a	n/a
12	CEBPB	chr13:50656966-50657388	MCF-7	breast:	n/a	chr13:50657130-50657141 chr13:50657131-50657140 chr13:50657129-50657142
13	SMARCC1	chr13:50654995-50657413	Hela-S3	cervix:	n/a	n/a
14	CEBPB	chr13:50656583-50657428	K562	blood:	n/a	chr13:50657130-50657141 chr13:50657131-50657140 chr13:50657129-50657142
15	MXI1	chr13:50654083-50657380	IMR90	lung:	n/a	n/a
16	CEBPB	chr13:50656713-50657381	A549	lung:	n/a	chr13:50657130-50657141 chr13:50657131-50657140 chr13:50657129-50657142
17	MXI1	chr13:50654074-50657477	SK-N-SH	brain:	n/a	n/a
18	TEAD4	chr13:50655550-50657384	K562	blood:	n/a	n/a
19	ARID3A	chr13:50656024-50657397	HepG2	liver:	n/a	chr13:50656187-50656202

No.	Distal block	Cell Line	Cell type
1	chr13:50652169..50667024-chr13:50693268..50703943,57	K562	blood:
2	chr13:50656933..50657634-chr13:51485862..51486382,2	K562	blood:
3	chr13:50569852..50573038-chr13:50651628..50659276,11	K562	blood:
4	chr13:50653265..50655572-chr13:50657148..50659226,2	MCF-7	breast:
5	chr13:50569748..50573186-chr13:50654848..50657793,4	MCF-7	breast:
6	chr13:50656878..50660410-chr13:50670774..50674010,3	K562	blood:
7	chr13:50653006..50665770-chr13:50696335..50703879,43	K562	blood:
8	chr13:50657111..50659219-chr13:51482850..51485149,3	MCF-7	breast:
9	chr13:50569462..50575212-chr13:50651363..50657415,15	K562	blood:
10	chr13:50654073..50663597-chr13:50696674..50702768,25	MCF-7	breast:
11	chr13:50654380..50657403-chr13:51482897..51486295,4	K562	blood:
12	chr13:50652189..50666968-chr13:50693462..50701392,46	MCF-7	breast:

Variant related genes	Relation type
DLEU2	TF binding region
ENSG00000233672	Chromatin interaction
ENSG00000136104	Chromatin interaction
ENSG00000264864	Chromatin interaction
ENSG00000214359	Chromatin interaction
ENSG00000204977	Chromatin interaction
ENSG00000231607	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1043208	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10492746	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1063181	0.84[ASN][1000 genomes]
rs1063183	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs12100038	0.84[ASN][1000 genomes]
rs12583615	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12583637	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12583652	1.00[ASN][1000 genomes]
rs12583823	0.95[ASN][1000 genomes]
rs12584069	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12585753	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1323451	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17073655	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17073682	1.00[ASN][1000 genomes]
rs17073724	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17073826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs17073834	0.86[EUR][1000 genomes]
rs17471092	0.90[EUR][1000 genomes]
rs1807033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2066540	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2066546	1.00[ASN][1000 genomes]
rs2066547	1.00[ASN][1000 genomes]
rs2066552	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2066553	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2066555	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2066559	1.00[ASN][1000 genomes]
rs2066562	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066565	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066566	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177313	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2181268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2407881	0.95[ASN][1000 genomes]
rs2407882	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs41308548	0.84[ASN][1000 genomes]
rs4614628	0.81[AFR][1000 genomes]
rs55638467	0.84[ASN][1000 genomes]
rs55727821	0.84[ASN][1000 genomes]
rs55869555	0.84[ASN][1000 genomes]
rs57230741	0.95[ASN][1000 genomes]
rs59931782	0.95[ASN][1000 genomes]
rs60583460	1.00[ASN][1000 genomes]
rs60828549	0.86[ASN][1000 genomes]
rs60926548	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960442	0.84[ASN][1000 genomes]
rs61960445	0.84[ASN][1000 genomes]
rs61960446	0.84[ASN][1000 genomes]
rs61960447	0.83[AFR][1000 genomes]
rs61960449	0.84[ASN][1000 genomes]
rs61960450	0.84[ASN][1000 genomes]
rs61960451	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61960454	0.95[ASN][1000 genomes]
rs61960455	0.95[ASN][1000 genomes]
rs61960457	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61961261	0.95[ASN][1000 genomes]
rs61961263	0.95[ASN][1000 genomes]
rs61961294	1.00[ASN][1000 genomes]
rs61961298	1.00[ASN][1000 genomes]
rs61961299	1.00[ASN][1000 genomes]
rs61961301	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61961302	1.00[ASN][1000 genomes]
rs61961303	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61961304	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961305	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961306	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61961323	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961324	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961325	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961327	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961328	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61962359	0.88[EUR][1000 genomes]
rs6561571	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6561572	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6561575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561576	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66559968	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66756338	1.00[ASN][1000 genomes]
rs7140070	0.81[EUR][1000 genomes]
rs7319351	0.95[ASN][1000 genomes]
rs73196708	0.84[ASN][1000 genomes]
rs73196731	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73196734	1.00[ASN][1000 genomes]
rs73196744	0.95[ASN][1000 genomes]
rs73196768	0.86[EUR][1000 genomes]
rs7325091	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs7325993	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs732729	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7328892	0.84[ASN][1000 genomes]
rs7331247	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7334063	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7336477	0.95[ASN][1000 genomes]
rs7336927	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7339181	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790944	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7981648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7982125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7984332	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7984907	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7986364	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7986432	0.95[ASN][1000 genomes]
rs7990502	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7991454	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs7991744	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7992903	0.95[ASN][1000 genomes]
rs7994224	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7995557	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7997305	0.95[ASN][1000 genomes]
rs7997402	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7997638	1.00[ASN][1000 genomes]
rs7998223	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998391	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9596240	0.86[EUR][1000 genomes]
rs9670083	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers 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	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12100048	TRIM13	Cis_1M	lymphoblastoid	RTeQTL
rs12100048	ENSG00000176124	cis	multi-tissue	Pritchard
rs12100048	DLEU1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50648400-50657400	Active TSS	GM12878-XiMat	blood
2	chr13:50651800-50658200	Active TSS	HMEC	breast
3	chr13:50651800-50659600	Active TSS	K562	blood
4	chr13:50652200-50658000	Active TSS	HSMMtube	muscle
5	chr13:50652400-50657400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr13:50652400-50657400	Active TSS	Psoas Muscle	Psoas
7	chr13:50652400-50657600	Active TSS	Thymus	Thymus
8	chr13:50652400-50658000	Active TSS	Hela-S3	cervix
9	chr13:50652600-50657400	Active TSS	HSMM	muscle
10	chr13:50652600-50657800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr13:50652600-50657800	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr13:50652800-50657800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr13:50652800-50657800	Active TSS	NHDF-Ad	bronchial
14	chr13:50652800-50658200	Active TSS	A549	lung
15	chr13:50653000-50657400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr13:50653000-50657800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr13:50653000-50658200	Active TSS	Fetal Intestine Large	intestine
18	chr13:50653000-50658200	Active TSS	NH-A	brain
19	chr13:50653200-50657800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr13:50653200-50657800	Active TSS	Fetal Heart	heart
21	chr13:50653200-50658000	Active TSS	NHLF	lung
22	chr13:50653400-50657400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr13:50653400-50657400	Active TSS	Right Atrium	heart
24	chr13:50653400-50658000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr13:50653600-50657400	Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr13:50653600-50657400	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr13:50653600-50657400	Active TSS	Fetal Muscle Trunk	muscle
28	chr13:50653600-50657800	Active TSS	Fetal Intestine Small	intestine
29	chr13:50653600-50658000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr13:50653800-50657400	Active TSS	H1 Cell Line	embryonic stem cell
31	chr13:50653800-50657600	Active TSS	Fetal Stomach	stomach
32	chr13:50653800-50657800	Active TSS	NHEK	skin
33	chr13:50653800-50658000	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr13:50654000-50657600	Active TSS	Placenta	Placenta
35	chr13:50654000-50657800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr13:50654000-50658200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr13:50654200-50657400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr13:50654200-50657400	Active TSS	H9 Cell Line	embryonic stem cell
39	chr13:50654200-50657400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr13:50654200-50657400	Active TSS	Left Ventricle	heart
41	chr13:50654200-50657400	Active TSS	Right Ventricle	heart
42	chr13:50654400-50657400	Active TSS	Esophagus	oesophagus
43	chr13:50654600-50657400	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr13:50654800-50657400	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr13:50654800-50657400	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr13:50655200-50657800	Active TSS	Liver	Liver
47	chr13:50655400-50657600	Active TSS	Dnd41	blood
48	chr13:50655400-50658000	Active TSS	Colonic Mucosa	Colon
49	chr13:50655600-50657400	Active TSS	Stomach Mucosa	stomach
50	chr13:50655600-50657800	Active TSS	Stomach Smooth Muscle	stomach

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