Variant report

Variant	rs9490166
Chromosome Location	chr6:121656320-121656321
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	IRF1	chr6:121655234-121657101	K562	blood:	n/a	chr6:121656078-121656092 chr6:121656077-121656091 chr6:121656078-121656098 chr6:121656083-121656097 chr6:121656086-121656096 chr6:121656080-121656094 chr6:121656082-121656096 chr6:121656035-121656044 chr6:121656080-121656091 chr6:121656080-121656101 chr6:121656079-121656091 chr6:121656079-121656091 chr6:121656086-121656097 chr6:121656079-121656096 chr6:121656081-121656092 chr6:121656048-121656059 chr6:121656084-121656097 chr6:121656087-121656098 chr6:121656084-121656097 chr6:121656078-121656091 chr6:121656080-121656090 chr6:121656076-121656090 chr6:121656079-121656093 chr6:121656086-121656100 chr6:121656084-121656097
2	TAL1	chr6:121655483-121656536	K562	blood:	n/a	n/a
3	MTA3	chr6:121655653-121656322	GM12878	blood:	n/a	n/a
4	PBX3	chr6:121655286-121656332	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr6:121655378-121656568	K562	blood:	n/a	n/a
6	POLR2A	chr6:121655367-121656781	Raji	blood:	n/a	n/a
7	POLR2A	chr6:121655364-121656362	Hela-S3	cervix:	n/a	n/a
8	CREB1	chr6:121655363-121656545	HepG2	liver:	n/a	chr6:121655915-121655928
9	MYC	chr6:121655420-121656362	NB4	blood:	n/a	n/a
10	PML	chr6:121655318-121656350	K562	blood:	n/a	n/a
11	TBL1XR1	chr6:121655653-121656375	K562	blood:	n/a	n/a
12	POLR2A	chr6:121655352-121656364	HCT-116	colon:	n/a	n/a
13	MAZ	chr6:121655352-121657021	IMR90	lung:	n/a	n/a
14	POLR2A	chr6:121655386-121656607	K562	blood:	n/a	n/a
15	POLR2A	chr6:121655283-121656393	U87	brain:	n/a	n/a
16	EP300	chr6:121655585-121656644	GM12878	blood:	n/a	chr6:121656081-121656095
17	RCOR1	chr6:121655350-121656811	K562	blood:	n/a	n/a
18	POLR2A	chr6:121655364-121656763	GM12891	blood:	n/a	n/a
19	POLR2A	chr6:121655277-121656398	U87	brain:	n/a	n/a
20	POLR2A	chr6:121655377-121656589	GM18505	blood:	n/a	n/a
21	MAX	chr6:121655366-121656348	SK-N-SH	brain:	n/a	n/a
22	WRNIP1	chr6:121655414-121656741	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:121655308-121656574	SK-N-SH	brain:	n/a	n/a
24	CUX1	chr6:121655204-121656760	K562	blood:	n/a	chr6:121656058-121656067
25	MXI1	chr6:121655221-121656900	IMR90	lung:	n/a	n/a
26	RELA	chr6:121655402-121656345	GM18951	blood:	n/a	n/a
27	CREB1	chr6:121655421-121656435	K562	blood:	n/a	chr6:121655915-121655928
28	RFX5	chr6:121655533-121656597	HepG2	liver:	n/a	n/a
29	EBF1	chr6:121655332-121656515	GM12878	blood:	n/a	n/a
30	POLR2A	chr6:121655368-121656597	HCT-116	colon:	n/a	n/a
31	MTA3	chr6:121655213-121656328	GM12878	blood:	n/a	n/a
32	POLR2A	chr6:121655404-121656437	HepG2	liver:	n/a	n/a
33	POLR2A	chr6:121655379-121656950	GM19099	blood:	n/a	n/a
34	BHLHE40	chr6:121655416-121656356	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:121655372-121656824	K562	blood:	n/a	n/a
36	POLR2A	chr6:121655321-121656396	PFSK-1	brain:	n/a	n/a
37	SIN3A	chr6:121655502-121656328	H1-hESC	embryonic stem cell:	n/a	chr6:121655696-121655709 chr6:121655719-121655730
38	RELA	chr6:121655423-121656499	GM10847	blood:	n/a	n/a
39	POLR2A	chr6:121655387-121656724	IMR90	lung:	n/a	n/a
40	POLR2A	chr6:121655336-121656541	H1-hESC	embryonic stem cell:	n/a	n/a
41	IRF1	chr6:121655398-121656548	K562	blood:	n/a	chr6:121656078-121656092 chr6:121656077-121656091 chr6:121656078-121656098 chr6:121656083-121656097 chr6:121656086-121656096 chr6:121656080-121656094 chr6:121656082-121656096 chr6:121656035-121656044 chr6:121656080-121656091 chr6:121656080-121656101 chr6:121656079-121656091 chr6:121656079-121656091 chr6:121656086-121656097 chr6:121656079-121656096 chr6:121656081-121656092 chr6:121656048-121656059 chr6:121656084-121656097 chr6:121656087-121656098 chr6:121656084-121656097 chr6:121656078-121656091 chr6:121656080-121656090 chr6:121656076-121656090 chr6:121656079-121656093 chr6:121656086-121656100 chr6:121656084-121656097
42	IRF4	chr6:121655459-121656324	GM12878	blood:	n/a	chr6:121656080-121656101 chr6:121656084-121656098
43	POLR2A	chr6:121655334-121656321	U87	brain:	n/a	n/a
44	POLR2A	chr6:121655390-121657236	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr6:121655366-121656806	PBDE	blood:	n/a	n/a
46	POLR2A	chr6:121655377-121656707	MCF10A-Er-Src	breast:	n/a	n/a
47	CEBPB	chr6:121655717-121656545	GM12878	blood:	n/a	n/a
48	MXI1	chr6:121655443-121656617	HepG2	liver:	n/a	n/a
49	POLR2A	chr6:121655369-121656354	ProgFib	skin:	n/a	n/a
50	ATF2	chr6:121655449-121656378	GM12878	blood:	n/a	chr6:121655914-121655928 chr6:121655916-121655927

Variant related genes	Relation type
TBC1D32	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs17083247	1.00[AMR][1000 genomes]
rs17083364	1.00[AMR][1000 genomes]
rs17083423	1.00[AMR][1000 genomes]
rs6569198	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6569199	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6905024	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6909602	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6918861	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6924917	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6929839	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6941053	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9482132	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9482133	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9482134	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9482135	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9482136	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9482138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9482140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9482141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9482142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9490168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9490169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9490171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9490172	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9490174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9490175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9490176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9490178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9490179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9490180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023384	chr6:121235867-121683448	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv530527	chr6:121298528-121789855	ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv830789	chr6:121581450-121732320	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:121653400-121656600	Active TSS	GM12878-XiMat	blood
2	chr6:121654400-121657000	Active TSS	Duodenum Mucosa	Duodenum
3	chr6:121654600-121656800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr6:121654600-121656800	Active TSS	A549	lung
5	chr6:121654800-121656400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:121654800-121656800	Active TSS	Rectal Mucosa Donor 31	rectum
7	chr6:121655000-121656400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:121655000-121656400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:121655000-121656400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:121655000-121656400	Active TSS	Brain Anterior Caudate	brain
11	chr6:121655000-121656400	Active TSS	Placenta	Placenta
12	chr6:121655000-121656400	Active TSS	Fetal Stomach	stomach
13	chr6:121655000-121656400	Active TSS	HSMM	muscle
14	chr6:121655000-121656600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr6:121655000-121656600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:121655000-121656600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:121655000-121656600	Active TSS	Psoas Muscle	Psoas
18	chr6:121655000-121656800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:121655000-121656800	Active TSS	Colonic Mucosa	Colon
20	chr6:121655200-121656400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:121655200-121656400	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr6:121655200-121656400	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr6:121655200-121656400	Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr6:121655200-121656400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:121655200-121656400	Active TSS	Brain Angular Gyrus	brain
26	chr6:121655200-121656400	Active TSS	Brain Hippocampus Middle	brain
27	chr6:121655200-121656400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr6:121655200-121656400	Active TSS	Fetal Intestine Small	intestine
29	chr6:121655200-121656400	Active TSS	Fetal Lung	lung
30	chr6:121655200-121656400	Active TSS	Thymus	Thymus
31	chr6:121655200-121656400	Active TSS	HMEC	breast
32	chr6:121655200-121656400	Active TSS	NHDF-Ad	bronchial
33	chr6:121655200-121656400	Active TSS	Osteobl	bone
34	chr6:121655200-121656600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:121655200-121656600	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr6:121655200-121656600	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr6:121655200-121656600	Active TSS	Aorta	Aorta
38	chr6:121655200-121656600	Active TSS	Colon Smooth Muscle	Colon
39	chr6:121655200-121656600	Active TSS	Fetal Brain Female	brain
40	chr6:121655200-121656600	Active TSS	Fetal Intestine Large	intestine
41	chr6:121655200-121656600	Active TSS	Right Ventricle	heart
42	chr6:121655200-121656600	Active TSS	Stomach Smooth Muscle	stomach
43	chr6:121655200-121656800	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr6:121655200-121656800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:121655200-121656800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:121655200-121656800	Active TSS	Brain Substantia Nigra	brain
47	chr6:121655200-121656800	Active TSS	HSMMtube	muscle
48	chr6:121655200-121657000	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr6:121655200-121657000	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr6:121655200-121657000	Active TSS	Rectal Smooth Muscle	rectum

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