Variant report

Variant	rs9398066
Chromosome Location	chr6:106546377-106546378
allele	A/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	POU2F2	chr6:106546369-106547137	GM12878	blood:	n/a	n/a
2	EGR1	chr6:106546294-106547100	HCT-116	colon:	n/a	chr6:106546685-106546694 chr6:106546645-106546658 chr6:106546683-106546697 chr6:106546681-106546696
3	POLR2A	chr6:106546373-106546663	ProgFib	skin:	n/a	n/a
4	POLR2A	chr6:106546231-106546957	K562	blood:	n/a	n/a
5	ARID3A	chr6:106545127-106546631	K562	blood:	n/a	n/a
6	POLR2A	chr6:106544976-106547443	GM19193	blood:	n/a	n/a
7	CREB1	chr6:106546368-106547108	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:106545483-106547876	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:106544957-106547891	GM18505	blood:	n/a	n/a
10	POLR2A	chr6:106545118-106547661	IMR90	lung:	n/a	n/a
11	POLR2A	chr6:106545196-106546872	PBDE	blood:	n/a	n/a
12	BHLHE40	chr6:106546365-106546992	GM12878	blood:	n/a	n/a
13	PML	chr6:106546368-106547079	GM12878	blood:	n/a	n/a
14	TBP	chr6:106545374-106546743	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr6:106546234-106547559	GM12892	blood:	n/a	n/a
16	FOXA2	chr6:106546357-106546808	A549	lung:	n/a	n/a
17	CHD2	chr6:106546341-106546908	GM12878	blood:	n/a	n/a
18	CTCF	chr6:106546340-106546490	AG10803	skin:	n/a	n/a
19	POLR2A	chr6:106546270-106547552	GM12892	blood:	n/a	n/a
20	KAP1	chr6:106545383-106547331	U2OS	brain:	n/a	n/a
21	FOXM1	chr6:106546309-106547051	GM12878	blood:	n/a	n/a
22	MYC	chr6:106545106-106547260	K562	blood:	n/a	chr6:106545824-106545834
23	TBL1XR1	chr6:106544969-106546776	K562	blood:	n/a	n/a
24	RELA	chr6:106545122-106546986	GM19193	blood:	n/a	n/a
25	TCF12	chr6:106545470-106546865	A549	lung:	n/a	n/a
26	RUNX3	chr6:106546372-106547029	GM12878	blood:	n/a	n/a
27	MYC	chr6:106545084-106546493	K562	blood:	n/a	chr6:106545824-106545834
28	POLR2A	chr6:106546179-106546892	HCT-116	colon:	n/a	n/a
29	POLR2A	chr6:106545183-106547894	GM12878	blood:	n/a	n/a
30	TAF1	chr6:106546297-106546967	K562	blood:	n/a	n/a
31	NFIC	chr6:106546219-106547396	GM12878	blood:	n/a	chr6:106546239-106546256
32	IKZF1	chr6:106545073-106547059	GM12878	blood:	n/a	n/a
33	KAP1	chr6:106545292-106547472	HEK293	kidney:	n/a	n/a
34	MTA3	chr6:106545287-106547201	GM12878	blood:	n/a	n/a
35	JUND	chr6:106545121-106547080	K562	blood:	n/a	chr6:106546772-106546782 chr6:106546773-106546781
36	TBP	chr6:106545147-106546955	GM12878	blood:	n/a	n/a
37	STAT3	chr6:106546309-106546923	MCF10A-Er-Src	breast:	n/a	n/a
38	MAZ	chr6:106546355-106546899	GM12878	blood:	n/a	n/a
39	POLR2A	chr6:106544453-106547850	GM19099	blood:	n/a	n/a
40	IRF1	chr6:106544996-106546885	K562	blood:	n/a	chr6:106545768-106545782 chr6:106546155-106546164 chr6:106545374-106545381
41	RELA	chr6:106546347-106547018	GM19099	blood:	n/a	n/a
42	EP300	chr6:106545158-106546990	GM12878	blood:	n/a	chr6:106546151-106546165 chr6:106546662-106546672 chr6:106546351-106546365 chr6:106545769-106545783 chr6:106545716-106545726
43	POLR2A	chr6:106546145-106547428	U87	brain:	n/a	n/a
44	POLR2A	chr6:106546318-106546915	K562	blood:	n/a	n/a
45	POLR2A	chr6:106545525-106547527	GM12892	blood:	n/a	n/a
46	MAX	chr6:106546373-106546872	K562	blood:	n/a	n/a
47	CEBPB	chr6:106545472-106547031	GM12878	blood:	n/a	n/a
48	HEY1	chr6:106546330-106546999	K562	blood:	n/a	n/a
49	MAZ	chr6:106546260-106547214	K562	blood:	n/a	n/a
50	RELA	chr6:106545044-106547010	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:106537562..106538454-chr6:106545596..106546468,2	HCT-116	colon:

Variant related genes	Relation type
ENSG00000269919	TF binding region
PRDM1	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12663005	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17558727	1.00[AMR][1000 genomes]
rs17558797	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2185379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3890556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6913893	0.81[AMR][1000 genomes]
rs9373830	0.85[AMR][1000 genomes]
rs9384600	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9386511	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9398059	0.85[AMR][1000 genomes]
rs9398063	1.00[AMR][1000 genomes]
rs9398065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1025231	chr6:106451012-106634389	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers 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 target site	9 gene(s)	inside rSNPs	diseases
3	nsv830755	chr6:106461705-106624202	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1025900	chr6:106529777-106898421	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1018270	chr6:106531658-106908606	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv538399	chr6:106531658-106908606	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv1832544	chr6:106539914-106642993	Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106542800-106548600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:106543600-106549600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:106544400-106546400	Flanking Active TSS	Dnd41	blood
4	chr6:106544600-106546600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr6:106544600-106548000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr6:106544800-106551200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:106545000-106546400	Active TSS	A549	lung
8	chr6:106545000-106546600	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr6:106545000-106547000	Flanking Active TSS	GM12878-XiMat	blood
10	chr6:106545000-106547400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr6:106545000-106547400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
12	chr6:106545000-106547400	Bivalent/Poised TSS	Liver	Liver
13	chr6:106545000-106547400	Active TSS	Rectal Smooth Muscle	rectum
14	chr6:106545000-106547600	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr6:106545000-106547600	Active TSS	Ovary	ovary
16	chr6:106545000-106548800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:106545000-106549200	Active TSS	Colonic Mucosa	Colon
18	chr6:106545200-106546400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:106545200-106546400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
20	chr6:106545200-106546400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:106545200-106546400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
22	chr6:106545200-106546400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:106545200-106546400	Active TSS	Duodenum Mucosa	Duodenum
24	chr6:106545200-106546600	Active TSS	Psoas Muscle	Psoas
25	chr6:106545200-106546800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:106545200-106546800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:106545200-106547000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:106545200-106547000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr6:106545200-106547000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:106545200-106547000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
31	chr6:106545200-106547000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
32	chr6:106545200-106547000	Active TSS	Stomach Mucosa	stomach
33	chr6:106545200-106547000	Flanking Active TSS	NH-A	brain
34	chr6:106545200-106547200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
35	chr6:106545200-106547400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
36	chr6:106545200-106547400	Flanking Active TSS	Osteobl	bone
37	chr6:106545200-106547600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
38	chr6:106545400-106546400	Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr6:106545400-106546400	Active TSS	Colon Smooth Muscle	Colon
40	chr6:106545400-106546400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr6:106545400-106546400	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr6:106545400-106546400	Active TSS	Left Ventricle	heart
43	chr6:106545400-106546400	Active TSS	Right Atrium	heart
44	chr6:106545400-106546400	Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr6:106545400-106546600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:106545400-106546600	Active TSS	NHLF	lung
47	chr6:106545400-106546800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:106545400-106546800	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr6:106545400-106547000	Bivalent/Poised TSS	Brain Substantia Nigra	brain
50	chr6:106545400-106547200	Active TSS	H9 Cell Line	embryonic stem cell

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