Variant report

Variant	rs1232392
Chromosome Location	chr6:13272671-13272672
allele	C/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	YY1	chr6:13272314-13273146	GM12878	blood:	n/a	chr6:13272842-13272853
2	EP300	chr6:13272364-13273223	GM12878	blood:	n/a	chr6:13272856-13272872
3	CHD2	chr6:13272402-13273404	GM12878	blood:	n/a	n/a
4	MTA3	chr6:13272472-13275024	GM12878	blood:	n/a	n/a
5	CEBPB	chr6:13272209-13272700	K562	blood:	n/a	chr6:13272448-13272459
6	RELA	chr6:13272352-13273287	GM18951	blood:	n/a	n/a
7	BHLHE40	chr6:13272403-13274607	K562	blood:	n/a	chr6:13272899-13272908 chr6:13272899-13272908 chr6:13272900-13272909 chr6:13272874-13272890 chr6:13272849-13272865 chr6:13272893-13272914
8	MAZ	chr6:13272420-13273362	GM12878	blood:	n/a	chr6:13272870-13272880
9	E2F6	chr6:13272598-13273150	K562	blood:	n/a	n/a
10	RCOR1	chr6:13272626-13273192	K562	blood:	n/a	n/a
11	FOXM1	chr6:13272658-13273207	GM12878	blood:	n/a	n/a
12	YY1	chr6:13272359-13273237	GM12878	blood:	n/a	chr6:13272842-13272853
13	YY1	chr6:13272416-13273116	GM12892	blood:	n/a	chr6:13272842-13272853
14	POLR2A	chr6:13272388-13273184	GM12891	blood:	n/a	n/a
15	POLR2A	chr6:13272298-13273272	GM19193	blood:	n/a	n/a
16	USF2	chr6:13272407-13273181	GM12878	blood:	n/a	chr6:13272899-13272908 chr6:13272899-13272908 chr6:13272900-13272909 chr6:13272874-13272890 chr6:13272849-13272865 chr6:13272893-13272914
17	MAX	chr6:13272344-13273697	NB4	blood:	n/a	chr6:13272870-13272880
18	JUN	chr6:13272018-13276804	K562	blood:	n/a	chr6:13276647-13276657
19	POLR2A	chr6:13272363-13273269	GM12878	blood:	n/a	n/a
20	SPI1	chr6:13272357-13273286	GM12878	blood:	n/a	chr6:13272922-13272935
21	RELA	chr6:13272294-13275127	GM12891	blood:	n/a	n/a
22	POLR2A	chr6:13271984-13273855	K562	blood:	n/a	n/a
23	RELA	chr6:13272249-13275025	GM19193	blood:	n/a	n/a
24	NFIC	chr6:13272658-13273319	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:13272496-13275011	GM19099	blood:	n/a	n/a
26	RELA	chr6:13272415-13276072	GM10847	blood:	n/a	n/a
27	TBL1XR1	chr6:13272326-13274866	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:13272223-13276600	GM12878	blood:	n/a	n/a
29	EBF1	chr6:13272378-13273311	GM12878	blood:	n/a	chr6:13272708-13272717 chr6:13272907-13272918
30	NR2F2	chr6:13272645-13276785	K562	blood:	n/a	n/a
31	STAT1	chr6:13272586-13273308	GM12878	blood:	n/a	n/a
32	PML	chr6:13272251-13275171	GM12878	blood:	n/a	n/a
33	RUNX3	chr6:13272292-13274947	GM12878	blood:	n/a	n/a
34	POLR2A	chr6:13272237-13275957	GM12892	blood:	n/a	n/a
35	POLR2A	chr6:13272526-13275090	GM18505	blood:	n/a	n/a
36	CREB1	chr6:13272150-13273211	GM12878	blood:	n/a	n/a
37	POLR2A	chr6:13272499-13273207	GM18951	blood:	n/a	n/a
38	MYC	chr6:13272462-13274998	K562	blood:	n/a	chr6:13272870-13272880
39	ATF2	chr6:13272505-13273506	GM12878	blood:	n/a	n/a
40	MXI1	chr6:13272324-13275420	GM12878	blood:	n/a	n/a
41	STAT5A	chr6:13272382-13275170	GM12878	blood:	n/a	chr6:13272427-13272439
42	ELK1	chr6:13272565-13273145	GM12878	blood:	n/a	n/a
43	PAX5	chr6:13272669-13273092	GM12878	blood:	n/a	n/a
44	MAX	chr6:13272386-13273765	GM12878	blood:	n/a	chr6:13272870-13272880
45	POLR2A	chr6:13272393-13273280	GM12892	blood:	n/a	n/a
46	TEAD4	chr6:13272318-13275177	K562	blood:	n/a	n/a
47	CUX1	chr6:13272670-13272677	K562	blood:	n/a	n/a
48	POLR2A	chr6:13272662-13273158	GM12878	blood:	n/a	n/a
49	BHLHE40	chr6:13272222-13275037	GM12878	blood:	n/a	chr6:13272899-13272908 chr6:13272899-13272908 chr6:13272900-13272909 chr6:13272874-13272890 chr6:13272849-13272865 chr6:13272893-13272914
50	POLR2A	chr6:13271496-13276674	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13268970..13278598-chr6:13326296..13332818,15	K562	blood:
2	chr6:13272205..13274313-chr6:13327989..13330165,3	K562	blood:

Variant related genes	Relation type
PHACTR1	TF binding region
ENSG00000145979	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1223397	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1223399	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1223400	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1223401	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1223402	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1223403	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13191897	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13205692	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17700321	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17767967	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2048552	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs20499	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs20500	0.83[EUR][1000 genomes]
rs34505804	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35511719	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35549743	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3734878	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3817737	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3817738	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3817741	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3817742	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs68050381	0.88[ASN][1000 genomes]
rs9357660	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9381884	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9395602	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13249800-13287000	Weak transcription	Fetal Brain Male	brain
2	chr6:13256600-13273200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:13256600-13278200	Weak transcription	Pancreas	Pancrea
4	chr6:13261400-13273000	Weak transcription	Adipose Nuclei	Adipose
5	chr6:13262600-13272800	Weak transcription	Primary T cells from cord blood	blood
6	chr6:13267000-13274200	Weak transcription	Gastric	stomach
7	chr6:13267400-13280400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:13267400-13283600	Weak transcription	Fetal Brain Female	brain
9	chr6:13268000-13278800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:13268000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:13269200-13282000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:13269400-13274200	Weak transcription	Aorta	Aorta
13	chr6:13269400-13275400	Weak transcription	Right Ventricle	heart
14	chr6:13269400-13284800	Weak transcription	Right Atrium	heart
15	chr6:13269600-13273000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:13269600-13273000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:13269600-13273200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:13269600-13275600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:13269600-13286600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr6:13269600-13286600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:13270200-13272800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:13270200-13273800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr6:13270200-13291600	Weak transcription	HSMM	muscle
24	chr6:13270400-13282000	Weak transcription	Ovary	ovary
25	chr6:13270400-13285400	Weak transcription	Fetal Heart	heart
26	chr6:13270600-13281000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr6:13270600-13283600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:13270800-13273400	Weak transcription	HSMMtube	muscle
29	chr6:13271600-13287200	Weak transcription	Fetal Lung	lung
30	chr6:13272000-13273000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:13272000-13273000	Flanking Active TSS	GM12878-XiMat	blood
32	chr6:13272000-13273800	Strong transcription	Stomach Smooth Muscle	stomach
33	chr6:13272000-13274000	Enhancers	Brain Substantia Nigra	brain
34	chr6:13272000-13275800	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr6:13272200-13272800	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr6:13272200-13273000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:13272200-13273000	Genic enhancers	Brain Angular Gyrus	brain
38	chr6:13272200-13273000	Strong transcription	Fetal Stomach	stomach
39	chr6:13272200-13273000	Strong transcription	Lung	lung
40	chr6:13272200-13273200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:13272200-13273200	Strong transcription	Left Ventricle	heart
42	chr6:13272200-13273400	Strong transcription	Brain Germinal Matrix	brain
43	chr6:13272200-13274400	Enhancers	Brain Anterior Caudate	brain
44	chr6:13272200-13274400	Enhancers	Brain Cingulate Gyrus	brain
45	chr6:13272200-13275800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr6:13272200-13276200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr6:13272400-13272800	Flanking Active TSS	Primary B cells from peripheral blood	blood
48	chr6:13272400-13272800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:13272400-13272800	Enhancers	Duodenum Mucosa	Duodenum
50	chr6:13272400-13272800	Enhancers	Spleen	Spleen

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