Variant report

Variant	rs2116023
Chromosome Location	chr7:150724803-150724804
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	chr7:150723712-150726126	K562	blood:	n/a	chr7:150725350-150725359
2	RCOR1	chr7:150723966-150726437	K562	blood:	n/a	n/a
3	MYC	chr7:150723630-150726253	K562	blood:	n/a	n/a
4	SIN3A	chr7:150724711-150726133	H1-hESC	embryonic stem cell:	n/a	n/a
5	HCFC1	chr7:150724710-150726264	Hela-S3	cervix:	n/a	n/a
6	BACH1	chr7:150724474-150724863	K562	blood:	n/a	n/a
7	MYC	chr7:150723115-150726136	K562	blood:	n/a	n/a
8	CUX1	chr7:150724468-150726134	K562	blood:	n/a	n/a
9	MAZ	chr7:150724572-150726314	IMR90	lung:	n/a	n/a
10	IRF1	chr7:150722909-150726094	K562	blood:	n/a	chr7:150725350-150725359
11	RCOR1	chr7:150724759-150726372	IMR90	lung:	n/a	n/a
12	STAT5A	chr7:150723850-150724844	K562	blood:	n/a	n/a
13	POLR2A	chr7:150723608-150726158	K562	blood:	n/a	n/a
14	TRIM28	chr7:150723374-150726189	K562	blood:	n/a	n/a
15	POLR2A	chr7:150724050-150726206	K562	blood:	n/a	n/a
16	CEBPD	chr7:150724074-150724943	K562	blood:	n/a	n/a
17	SMARCC1	chr7:150724540-150726280	Hela-S3	cervix:	n/a	n/a
18	MYC	chr7:150724661-150726226	A549	lung:	n/a	n/a
19	NR2F2	chr7:150723823-150724831	K562	blood:	n/a	n/a
20	POLR2A	chr7:150724566-150726145	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr7:150724152-150726153	PBDE	blood:	n/a	n/a
22	GATA2	chr7:150724040-150724930	K562	blood:	n/a	n/a
23	TBL1XR1	chr7:150723099-150724829	K562	blood:	n/a	n/a
24	EP300	chr7:150723324-150724825	K562	blood:	n/a	n/a
25	TEAD4	chr7:150724181-150726592	K562	blood:	n/a	n/a
26	ZNF384	chr7:150724633-150726580	K562	blood:	n/a	n/a
27	MAX	chr7:150722995-150726538	K562	blood:	n/a	n/a
28	POLR2A	chr7:150723040-150726571	K562	blood:	n/a	n/a
29	SIN3AK20	chr7:150724797-150726312	MCF-7	breast:	n/a	n/a
30	TEAD4	chr7:150724189-150726559	K562	blood:	n/a	n/a
31	USF1	chr7:150724800-150726068	K562	blood:	n/a	chr7:150725052-150725063
32	GATA3	chr7:150724681-150725049	T-47D	breast:	n/a	n/a
33	SREBP1	chr7:150724455-150726249	GM12878	blood:	n/a	n/a
34	CEBPD	chr7:150724234-150724933	K562	blood:	n/a	n/a
35	POLR2A	chr7:150724000-150725994	H1-hESC	embryonic stem cell:	n/a	n/a
36	MYC	chr7:150723819-150726192	K562	blood:	n/a	n/a
37	POLR2A	chr7:150724786-150726087	MCF10A-Er-Src	breast:	n/a	n/a
38	JUN	chr7:150722625-150726841	K562	blood:	n/a	chr7:150723212-150723222
39	ZNF274	chr7:150724283-150725055	K562	blood:	n/a	n/a
40	USF1	chr7:150724800-150725528	H1-hESC	embryonic stem cell:	n/a	chr7:150725052-150725063
41	ZC3H11A	chr7:150724777-150724813	K562	blood:	n/a	n/a
42	USF1	chr7:150724563-150725583	K562	blood:	n/a	chr7:150725052-150725063
43	CBX3	chr7:150722906-150726571	K562	blood:	n/a	n/a
44	TAL1	chr7:150723116-150724836	K562	blood:	n/a	n/a
45	SP1	chr7:150724803-150726292	HCT-116	colon:	n/a	chr7:150725520-150725531 chr7:150725379-150725391 chr7:150725379-150725391 chr7:150725380-150725389
46	MXI1	chr7:150724537-150726771	SK-N-SH	brain:	n/a	n/a
47	MXI1	chr7:150724113-150726101	K562	blood:	n/a	n/a
48	BHLHE40	chr7:150723704-150726148	K562	blood:	n/a	n/a
49	GATA1	chr7:150723194-150726151	PBDE	blood:	n/a	chr7:150725351-150725361 chr7:150723521-150723534
50	MAX	chr7:150724761-150724822	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:150718943..150723286-chr7:150723746..150726907,4	MCF-7	breast:
2	chr7:150722965..150724842-chr7:150872237..150873917,2	MCF-7	breast:
3	chr7:150719730..150723078-chr7:150724265..150726856,4	MCF-7	breast:
4	chr7:150713283..150718085-chr7:150719345..150725201,8	MCF-7	breast:
5	chr7:150687026..150688559-chr7:150724058..150726072,2	MCF-7	breast:

Variant related genes	Relation type
ABCB8	TF binding region
ATG9B	TF binding region
ENSG00000181652	Chromatin interaction
ENSG00000164867	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12539332	0.82[ASN][1000 genomes]
rs2303922	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303924	0.87[ASN][1000 genomes]
rs2303926	0.92[ASN][1000 genomes]
rs2373927	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35900662	0.92[ASN][1000 genomes]
rs4148848	0.87[ASN][1000 genomes]
rs61218626	0.85[ASN][1000 genomes]
rs6944859	0.91[ASN][1000 genomes]
rs6944935	0.92[ASN][1000 genomes]
rs6947821	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821419	chr7:150593315-150974269	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
2	nsv1022246	chr7:150619660-150779924	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv889465	chr7:150640285-150800823	Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1017863	chr7:150643928-150779924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv539197	chr7:150643928-150779924	Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
6	nsv1028645	chr7:150643928-150806534	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
7	nsv539198	chr7:150643928-150879259	Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
8	nsv889469	chr7:150657209-150747746	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv889471	chr7:150700946-150751590	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv526410	chr7:150714812-150775306	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2116023	ATG9B	cis	Thyroid	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150716200-150725000	Weak transcription	Right Atrium	heart
2	chr7:150720200-150725000	Enhancers	Placenta Amnion	Placenta Amnion
3	chr7:150721600-150725000	Enhancers	Placenta	Placenta
4	chr7:150722000-150725000	Weak transcription	Esophagus	oesophagus
5	chr7:150722600-150725000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:150722800-150725000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:150722800-150725000	Enhancers	HMEC	breast
8	chr7:150723200-150725200	Flanking Active TSS	K562	blood
9	chr7:150723400-150725000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:150723400-150725000	Weak transcription	HSMM	muscle
11	chr7:150724000-150725000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr7:150724000-150726600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:150724200-150726600	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr7:150724400-150725000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:150724400-150725000	Flanking Active TSS	NHEK	skin
16	chr7:150724400-150725200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
17	chr7:150724400-150725400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:150724400-150726400	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr7:150724400-150726400	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr7:150724600-150725000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:150724600-150725000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr7:150724600-150725000	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr7:150724600-150725000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr7:150724600-150725000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr7:150724600-150725000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr7:150724600-150725000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:150724600-150725000	Enhancers	Fetal Brain Male	brain
28	chr7:150724600-150725000	Enhancers	Small Intestine	intestine
29	chr7:150724600-150725200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr7:150724600-150725200	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr7:150724600-150725200	Flanking Active TSS	Fetal Lung	lung
32	chr7:150724600-150725200	Flanking Active TSS	Stomach Mucosa	stomach
33	chr7:150724600-150725200	Flanking Active TSS	Hela-S3	cervix
34	chr7:150724600-150725400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr7:150724600-150725800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr7:150724600-150725800	Bivalent/Poised TSS	HepG2	liver
37	chr7:150724600-150726400	Active TSS	H9 Cell Line	embryonic stem cell
38	chr7:150724600-150726400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr7:150724800-150725000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr7:150724800-150725000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr7:150724800-150725000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:150724800-150725000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr7:150724800-150725000	Enhancers	Muscle Satellite Cultured Cells	--
44	chr7:150724800-150725000	Flanking Active TSS	Colon Smooth Muscle	Colon
45	chr7:150724800-150725000	Enhancers	Fetal Heart	heart
46	chr7:150724800-150725000	Flanking Active TSS	Fetal Intestine Large	intestine
47	chr7:150724800-150725000	Enhancers	Fetal Muscle Trunk	muscle
48	chr7:150724800-150725000	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr7:150724800-150725000	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr7:150724800-150725000	Flanking Active TSS	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links