Variant report

Variant	rs542274416
Chromosome Location	chr9:71939750-71939751
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	EGR1	chr9:71939730-71940170	ECC-1	luminal epithelium:	n/a	chr9:71940125-71940149
2	TCF12	chr9:71939651-71940361	ECC-1	luminal epithelium:	n/a	chr9:71940254-71940264
3	MAX	chr9:71939343-71940350	H1-hESC	embryonic stem cell:	n/a	chr9:71940260-71940269 chr9:71940289-71940299
4	HDAC2	chr9:71939415-71940308	MCF-7	breast:	n/a	n/a
5	POLR2A	chr9:71939460-71939832	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr9:71939400-71939911	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF143	chr9:71939413-71939798	H1-hESC	embryonic stem cell:	n/a	n/a
8	KAP1	chr9:71939400-71940134	HEK293	kidney:	n/a	chr9:71939736-71939744
9	MAX	chr9:71939215-71940286	HCT-116	colon:	n/a	chr9:71940260-71940269
10	MAX	chr9:71939328-71940369	H1-hESC	embryonic stem cell:	n/a	chr9:71940260-71940269 chr9:71940289-71940299
11	SIN3A	chr9:71939340-71941514	H1-hESC	embryonic stem cell:	n/a	chr9:71939943-71939956 chr9:71940048-71940061
12	ZBTB7A	chr9:71939486-71940317	ECC-1	luminal epithelium:	n/a	chr9:71940295-71940303 chr9:71939687-71939695
13	SIN3AK20	chr9:71939350-71939969	H1-hESC	embryonic stem cell:	n/a	n/a
14	MXI1	chr9:71939389-71940163	H1-hESC	embryonic stem cell:	n/a	n/a
15	EP300	chr9:71939316-71940840	ECC-1	luminal epithelium:	n/a	chr9:71940177-71940193 chr9:71940486-71940502 chr9:71940180-71940196 chr9:71940022-71940038
16	POLR2A	chr9:71939352-71940273	H1-hESC	embryonic stem cell:	n/a	n/a
17	CREB1	chr9:71939374-71940226	H1-hESC	embryonic stem cell:	n/a	chr9:71939809-71939822
18	POLR2A	chr9:71939665-71940328	ECC-1	luminal epithelium:	n/a	n/a
19	MAX	chr9:71939347-71940331	MCF-7	breast:	n/a	chr9:71940260-71940269 chr9:71940289-71940299
20	POLR2A	chr9:71939434-71940288	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr9:71939176-71940373	H1-hESC	embryonic stem cell:	n/a	n/a
22	TAF1	chr9:71939341-71940245	H1-hESC	embryonic stem cell:	n/a	n/a
23	BRCA1	chr9:71939386-71939797	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr9:71939319-71940421	ECC-1	luminal epithelium:	n/a	chr9:71940260-71940269 chr9:71940289-71940299
25	TBP	chr9:71939336-71940217	H1-hESC	embryonic stem cell:	n/a	n/a
26	NANOG	chr9:71939401-71939843	H1-hESC	embryonic stem cell:	n/a	n/a
27	GABPA	chr9:71939518-71940233	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr9:71939328-71940693	H1-hESC	embryonic stem cell:	n/a	n/a
29	E2F6	chr9:71939292-71940238	H1-hESC	embryonic stem cell:	n/a	chr9:71939929-71939940 chr9:71940063-71940073
30	MYC	chr9:71939704-71940307	MCF-7	breast:	n/a	chr9:71940260-71940269 chr9:71940289-71940299
31	MAX	chr9:71939334-71940305	HCT-116	colon:	n/a	chr9:71940260-71940269 chr9:71940289-71940299
32	E2F6	chr9:71939397-71939840	A549	lung:	n/a	n/a
33	RAD21	chr9:71939290-71940131	H1-hESC	embryonic stem cell:	n/a	chr9:71939998-71940012 chr9:71939996-71940010
34	TAF7	chr9:71939277-71940276	H1-hESC	embryonic stem cell:	n/a	n/a
35	JUND	chr9:71939401-71939988	H1-hESC	embryonic stem cell:	n/a	n/a
36	ZNF263	chr9:71939402-71940751	HEK293-T-REx	kidney:	n/a	chr9:71940097-71940118
37	ZBTB7A	chr9:71939438-71940228	ECC-1	luminal epithelium:	n/a	chr9:71939687-71939695
38	EGR1	chr9:71939616-71940224	ECC-1	luminal epithelium:	n/a	chr9:71940125-71940149
39	POLR2A	chr9:71939321-71940797	MCF-7	breast:	n/a	n/a
40	SMARCB1	chr9:71939441-71940788	Hela-S3	cervix:	n/a	n/a
41	E2F6	chr9:71939189-71940270	H1-hESC	embryonic stem cell:	n/a	chr9:71939929-71939940 chr9:71940063-71940073
42	POLR2A	chr9:71939495-71940662	MCF-7	breast:	n/a	n/a
43	MAX	chr9:71939361-71940324	ECC-1	luminal epithelium:	n/a	chr9:71940260-71940269 chr9:71940289-71940299
44	POLR2A	chr9:71939454-71940621	MCF-7	breast:	n/a	n/a
45	POLR2A	chr9:71939720-71940320	Gliobla	brain:	n/a	n/a
46	HA-E2F1	chr9:71939219-71940234	MCF-7	breast:	n/a	chr9:71939929-71939940 chr9:71940063-71940073

No.	Distal block	Cell Line	Cell type
1	chr9:71939667..71941572-chr9:71995013..71999921,5	MCF-7	breast:
2	chr9:71810860..71813115-chr9:71939521..71941834,2	MCF-7	breast:
3	chr9:71937269..71941011-chr9:72000572..72004392,4	MCF-7	breast:
4	chr9:71938510..71941284-chr9:71942079..71947019,4	MCF-7	breast:

Variant related genes	Relation type
FAM189A2	TF binding region
ENSG00000135063	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
6	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv893428	chr9:71926658-72027641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3374800	chr9:71939157-71942005	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv3417138	chr9:71939382-71941480	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71937600-71942800	Active TSS	Fetal Heart	heart
2	chr9:71938800-71940800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr9:71938800-71940800	Active TSS	Brain Substantia Nigra	brain
4	chr9:71938800-71941400	Active TSS	Brain Anterior Caudate	brain
5	chr9:71938800-71942800	Active TSS	Right Atrium	heart
6	chr9:71939000-71940600	Bivalent/Poised TSS	Fetal Lung	lung
7	chr9:71939000-71940800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
8	chr9:71939000-71941000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr9:71939000-71941000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr9:71939000-71941200	Active TSS	Ovary	ovary
11	chr9:71939000-71941400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr9:71939000-71942800	Active TSS	Stomach Smooth Muscle	stomach
13	chr9:71939200-71939800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
14	chr9:71939200-71940000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
15	chr9:71939200-71940600	Active TSS	Brain Hippocampus Middle	brain
16	chr9:71939200-71940600	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr9:71939200-71940800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
18	chr9:71939200-71940800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr9:71939200-71941000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr9:71939200-71941200	Active TSS	H9 Cell Line	embryonic stem cell
21	chr9:71939200-71941400	Active TSS	Left Ventricle	heart
22	chr9:71939200-71944000	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr9:71939400-71939800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
24	chr9:71939400-71939800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr9:71939400-71939800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr9:71939400-71939800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
27	chr9:71939400-71939800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
28	chr9:71939400-71939800	Flanking Bivalent TSS/Enh	Placenta	Placenta
29	chr9:71939400-71939800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
30	chr9:71939400-71939800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr9:71939400-71939800	Flanking Active TSS	Right Ventricle	heart
32	chr9:71939400-71939800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr9:71939400-71939800	Flanking Bivalent TSS/Enh	HepG2	liver
34	chr9:71939400-71940000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:71939400-71940000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr9:71939400-71940000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:71939400-71940000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:71939400-71940000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr9:71939400-71940000	Flanking Active TSS	Brain Cingulate Gyrus	brain
40	chr9:71939400-71940000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
41	chr9:71939400-71940000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
42	chr9:71939400-71940000	Bivalent Enhancer	Fetal Brain Male	brain
43	chr9:71939400-71940000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
44	chr9:71939400-71940000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
45	chr9:71939400-71940000	Bivalent/Poised TSS	Fetal Thymus	thymus
46	chr9:71939400-71940000	Bivalent Enhancer	Small Intestine	intestine
47	chr9:71939400-71940000	Flanking Active TSS	HMEC	breast
48	chr9:71939400-71940000	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
49	chr9:71939400-71940000	Bivalent Enhancer	NHDF-Ad	bronchial
50	chr9:71939400-71940000	Flanking Bivalent TSS/Enh	NHEK	skin

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