Variant report

Variant	rs72939433
Chromosome Location	chr6:106958726-106958727
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	SIN3A	chr6:106958413-106958799	GM12878	blood:	n/a	chr6:106958644-106958655
2	KAP1	chr6:106958538-106958898	HEK293	kidney:	n/a	n/a
3	BCLAF1	chr6:106958311-106958873	GM12878	blood:	n/a	chr6:106958646-106958659
4	E2F4	chr6:106958493-106958887	GM12878	blood:	n/a	n/a
5	CHD2	chr6:106958453-106958836	GM12878	blood:	n/a	n/a
6	MTA3	chr6:106958449-106959016	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:106957807-106960924	MCF10A-Er-Src	breast:	n/a	n/a
8	MAX	chr6:106957760-106958927	NB4	blood:	n/a	chr6:106958601-106958611
9	SMC3	chr6:106958418-106958774	GM12878	blood:	n/a	chr6:106958420-106958430
10	POLR2A	chr6:106958055-106958997	PANC-1	pancreas:	n/a	n/a
11	MAX	chr6:106958119-106958960	A549	lung:	n/a	chr6:106958601-106958611
12	REST	chr6:106958045-106958845	HL-60	blood:	n/a	chr6:106958112-106958125 chr6:106958366-106958379
13	MAX	chr6:106958258-106958878	MCF-7	breast:	n/a	chr6:106958601-106958611
14	MXI1	chr6:106957694-106959152	SK-N-SH	brain:	n/a	n/a
15	CTBP2	chr6:106957957-106958900	H1-hESC	embryonic stem cell:	n/a	n/a
16	EP300	chr6:106958573-106958773	HepG2	liver:	n/a	n/a
17	MYC	chr6:106957750-106958858	NB4	blood:	n/a	chr6:106958601-106958611
18	KAP1	chr6:106958628-106958811	U2OS	brain:	n/a	n/a
19	ZEB1	chr6:106958349-106958913	GM12878	blood:	n/a	n/a
20	ZNF143	chr6:106958410-106958827	GM12878	blood:	n/a	chr6:106958476-106958494
21	TEAD4	chr6:106958305-106958744	H1-hESC	embryonic stem cell:	n/a	n/a
22	MTA3	chr6:106958286-106958942	GM12878	blood:	n/a	n/a
23	PAX5	chr6:106958324-106958726	GM12892	blood:	n/a	n/a
24	POLR2A	chr6:106958311-106958806	SK-N-MC	brain:	n/a	n/a
25	MXI1	chr6:106958338-106958931	GM12878	blood:	n/a	n/a
26	MYC	chr6:106957904-106958977	MCF10A-Er-Src	breast:	n/a	chr6:106958601-106958611
27	USF2	chr6:106958622-106958791	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr6:106958001-106958867	NB4	blood:	n/a	n/a
29	HDAC2	chr6:106958414-106958782	HepG2	liver:	n/a	n/a
30	STAT3	chr6:106958701-106958998	MCF10A-Er-Src	breast:	n/a	n/a
31	ZEB1	chr6:106958258-106959008	HepG2	liver:	n/a	n/a
32	MYC	chr6:106958510-106959102	MCF10A-Er-Src	breast:	n/a	chr6:106958601-106958611
33	E2F6	chr6:106958167-106958835	A549	lung:	n/a	chr6:106958287-106958299
34	POLR2A	chr6:106958409-106958804	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr6:106958379-106958938	MCF10A-Er-Src	breast:	n/a	n/a
36	RUNX3	chr6:106958273-106958873	GM12878	blood:	n/a	n/a
37	MAX	chr6:106958328-106958794	ECC-1	luminal epithelium:	n/a	chr6:106958601-106958611
38	RCOR1	chr6:106958454-106958959	GM12878	blood:	n/a	n/a
39	MAZ	chr6:106958448-106958737	GM12878	blood:	n/a	n/a
40	SP1	chr6:106958502-106958862	GM12878	blood:	n/a	n/a
41	ELF1	chr6:106958060-106958849	GM12878	blood:	n/a	n/a
42	RAD21	chr6:106958430-106958727	SK-N-SH_RA	brain:	n/a	n/a
43	E2F4	chr6:106957768-106959295	MCF10A-Er-Src	breast:	n/a	chr6:106958287-106958299
44	SIN3AK20	chr6:106958076-106958962	PANC-1	pancreas:	n/a	n/a
45	MAX	chr6:106958339-106958837	ECC-1	luminal epithelium:	n/a	chr6:106958601-106958611
46	TAF1	chr6:106958477-106958770	SK-N-SH	brain:	n/a	n/a
47	CEBPB	chr6:106958588-106958835	H1-hESC	embryonic stem cell:	n/a	n/a
48	ELF1	chr6:106958117-106958897	GM12878	blood:	n/a	n/a
49	PML	chr6:106958294-106958915	GM12878	blood:	n/a	n/a
50	ZNF263	chr6:106958279-106958969	HEK293-T-REx	kidney:	n/a	chr6:106958846-106958855 chr6:106958689-106958698

No.	Distal block	Cell Line	Cell type
1	chr6:106955204..106959628-chr6:106966256..106969365,4	K562	blood:
2	chr6:106957571..106959305-chr6:106960058..106962439,2	MCF-7	breast:
3	chr6:106956358..106959318-chr6:106991274..106994095,2	MCF-7	breast:

Variant related genes	Relation type
AIM1	TF binding region
ENSG00000112297	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17495053	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17495248	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17495512	0.92[AMR][1000 genomes]
rs17495623	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17495678	0.92[AMR][1000 genomes]
rs17495742	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs61741114	0.86[AFR][1000 genomes]
rs66465674	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72939427	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72939431	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72939434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72939435	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72939440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72939443	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72941307	0.86[AFR][1000 genomes]
rs72941326	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1025510	chr6:106791080-106982400	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv538404	chr6:106791080-106982400	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106956800-106959600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr6:106957000-106959200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr6:106957000-106962800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:106957200-106958800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr6:106957200-106958800	Weak transcription	Hela-S3	cervix
6	chr6:106957200-106960000	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr6:106957200-106961200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
8	chr6:106957200-106961600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr6:106957200-106962800	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr6:106957400-106958800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr6:106957400-106958800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr6:106957400-106958800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:106957400-106959000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:106957400-106959000	Flanking Active TSS	Thymus	Thymus
15	chr6:106957400-106959200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr6:106957400-106959400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr6:106957400-106959800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
18	chr6:106957400-106960200	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr6:106957400-106962200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:106957400-106963400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr6:106957600-106958800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:106957600-106958800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
23	chr6:106957600-106959000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:106957600-106959000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
25	chr6:106957600-106959000	Active TSS	Rectal Smooth Muscle	rectum
26	chr6:106957600-106959000	Flanking Bivalent TSS/Enh	NH-A	brain
27	chr6:106957600-106959600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr6:106957600-106959800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr6:106957600-106961000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr6:106957800-106958800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:106957800-106958800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:106957800-106958800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
33	chr6:106957800-106959000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:106957800-106959000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
35	chr6:106957800-106959000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
36	chr6:106957800-106959000	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
37	chr6:106957800-106959000	Flanking Bivalent TSS/Enh	Osteobl	bone
38	chr6:106957800-106959400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr6:106957800-106959600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:106957800-106959800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr6:106957800-106961400	Active TSS	Right Atrium	heart
42	chr6:106958000-106958800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:106958000-106958800	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:106958000-106958800	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:106958000-106958800	Active TSS	Primary T cells from cord blood	blood
46	chr6:106958000-106958800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
47	chr6:106958000-106958800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr6:106958000-106958800	Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr6:106958000-106958800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:106958000-106958800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain

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