Variant report

Variant	rs59680363
Chromosome Location	chr7:98979451-98979452
allele	C/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	POLR2A	chr7:98976609-98979475	GM12892	blood:	n/a	n/a
2	HNF4G	chr7:98979050-98979637	HepG2	liver:	n/a	chr7:98979417-98979431
3	MXI1	chr7:98978625-98979968	SK-N-SH	brain:	n/a	chr7:98979641-98979650
4	MAX	chr7:98978472-98979596	HepG2	liver:	n/a	chr7:98979002-98979012 chr7:98978961-98978968
5	ELF1	chr7:98979264-98979505	HepG2	liver:	n/a	n/a
6	MXI1	chr7:98978176-98979613	HepG2	liver:	n/a	n/a
7	POLR2A	chr7:98976628-98979715	GM15510	blood:	n/a	n/a
8	MAX	chr7:98978131-98979860	HepG2	liver:	n/a	chr7:98979002-98979012 chr7:98978961-98978968 chr7:98978274-98978283
9	HMGN3	chr7:98979294-98979641	K562	blood:	n/a	n/a
10	POLR2A	chr7:98976592-98979794	GM12891	blood:	n/a	n/a
11	POLR2A	chr7:98978779-98979711	HepG2	liver:	n/a	n/a
12	POLR2A	chr7:98977475-98979823	K562	blood:	n/a	n/a
13	HNF4A	chr7:98979170-98979568	HepG2	liver:	n/a	chr7:98979417-98979431
14	POLR2A	chr7:98976610-98979794	GM18505	blood:	n/a	n/a
15	POLR2A	chr7:98977497-98979791	GM12878	blood:	n/a	n/a
16	POLR2A	chr7:98976834-98979870	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr7:98976659-98979619	GM12878	blood:	n/a	n/a
18	STAT5A	chr7:98976702-98980298	GM12878	blood:	n/a	chr7:98979486-98979498 chr7:98979431-98979443
19	POLR2A	chr7:98978333-98979724	HepG2	liver:	n/a	n/a
20	POLR2A	chr7:98979186-98979748	A549	lung:	n/a	n/a
21	POLR2A	chr7:98976524-98979851	GM12892	blood:	n/a	n/a
22	POLR2A	chr7:98976590-98979821	GM12878	blood:	n/a	n/a
23	ELF1	chr7:98977524-98979700	GM12878	blood:	n/a	chr7:98977917-98977930
24	POLR2A	chr7:98976454-98979886	GM12878	blood:	n/a	n/a
25	POLR2A	chr7:98976819-98980079	K562	blood:	n/a	n/a
26	POLR2A	chr7:98979132-98979729	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr7:98976852-98979487	K562	blood:	n/a	n/a
28	POLR2A	chr7:98979181-98979670	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr7:98978420-98979543	HepG2	liver:	n/a	n/a
30	POLR2A	chr7:98976645-98979831	GM12891	blood:	n/a	n/a
31	POLR2A	chr7:98976855-98979782	GM19193	blood:	n/a	n/a
32	POLR2A	chr7:98977287-98979572	K562	blood:	n/a	n/a
33	POLR2A	chr7:98979388-98979539	A549	lung:	n/a	n/a
34	POLR2A	chr7:98978242-98979981	HepG2	liver:	n/a	n/a
35	POLR2A	chr7:98976767-98979847	GM12891	blood:	n/a	n/a
36	POLR2A	chr7:98977893-98979720	HepG2	liver:	n/a	n/a
37	POLR2A	chr7:98978125-98979553	HepG2	liver:	n/a	n/a
38	NFATC1	chr7:98977498-98979839	GM12878	blood:	n/a	n/a
39	HNF4A	chr7:98978400-98979657	HepG2	liver:	n/a	chr7:98978574-98978588 chr7:98978571-98978583 chr7:98979417-98979431 chr7:98978575-98978587 chr7:98978573-98978588
40	POLR2A	chr7:98977615-98979745	A549	lung:	n/a	n/a
41	POLR2A	chr7:98977495-98979805	GM12878	blood:	n/a	n/a
42	POLR2A	chr7:98976541-98979945	GM12892	blood:	n/a	n/a
43	RAD21	chr7:98979355-98979517	HepG2	liver:	n/a	n/a
44	TBP	chr7:98979191-98979582	HepG2	liver:	n/a	n/a
45	HNF4A	chr7:98979183-98979594	HepG2	liver:	n/a	chr7:98979417-98979431
46	RCOR1	chr7:98979254-98979593	HepG2	liver:	n/a	n/a
47	HNF4G	chr7:98979158-98979622	HepG2	liver:	n/a	chr7:98979417-98979431
48	POLR2A	chr7:98977479-98979820	PANC-1	pancreas:	n/a	n/a
49	EP300	chr7:98978933-98980432	SK-N-SH	brain:	n/a	n/a
50	HEY1	chr7:98979175-98979623	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:98975447..98980936-chr7:99003746..99008536,8	MCF-7	breast:
2	chr7:98977788..98980375-chr7:98980403..98983687,6	MCF-7	breast:
3	chr7:98979371..98979879-chr7:98993328..98994292,2	MCF-7	breast:
4	chr7:98977857..98980973-chr7:99035179..99039094,4	MCF-7	breast:
5	chr7:98978155..98981581-chr7:99004279..99007902,6	MCF-7	breast:
6	chr7:98978815..98981136-chr7:98984654..98987297,2	MCF-7	breast:
7	chr7:98966478..98969149-chr7:98977868..98979453,2	MCF-7	breast:
8	chr7:98978195..98983060-chr7:98988487..98993755,6	MCF-7	breast:

Variant related genes	Relation type
ARPC1B	TF binding region
ENSG00000160917	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000106244	Chromatin interaction
ENSG00000130429	Chromatin interaction
ENSG00000106245	Chromatin interaction

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

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

rs_ID	r²[population]
rs10429050	1.00[AMR][1000 genomes]
rs45469701	1.00[AMR][1000 genomes]
rs45486103	1.00[AMR][1000 genomes]
rs45518537	1.00[AMR][1000 genomes]
rs45536437	1.00[AMR][1000 genomes]
rs45609448	1.00[AMR][1000 genomes]
rs59460511	1.00[AMR][1000 genomes]
rs61538655	1.00[AMR][1000 genomes]
rs61735345	1.00[AMR][1000 genomes]
rs73710450	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73710451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73710454	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73710455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73711206	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73711211	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs740159	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	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98971000-98990400	Weak transcription	Fetal Kidney	kidney
2	chr7:98973400-98984000	Weak transcription	Aorta	Aorta
3	chr7:98973400-98984200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:98973400-98984200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:98973400-98984200	Weak transcription	Ovary	ovary
6	chr7:98973400-98984400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr7:98973400-98987400	Weak transcription	Brain Germinal Matrix	brain
8	chr7:98973400-98987800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:98973400-98989800	Weak transcription	Brain Angular Gyrus	brain
10	chr7:98974800-98979800	Strong transcription	Fetal Intestine Small	intestine
11	chr7:98976800-98979800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr7:98977000-98979600	Genic enhancers	Muscle Satellite Cultured Cells	--
13	chr7:98977000-98979600	Enhancers	Esophagus	oesophagus
14	chr7:98977000-98979800	Enhancers	Fetal Muscle Trunk	muscle
15	chr7:98977200-98979800	Enhancers	Left Ventricle	heart
16	chr7:98977600-98979600	Enhancers	Fetal Heart	heart
17	chr7:98977600-98979600	Genic enhancers	Gastric	stomach
18	chr7:98977800-98979600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:98977800-98979600	Enhancers	Right Atrium	heart
20	chr7:98977800-98979800	Enhancers	Right Ventricle	heart
21	chr7:98977800-98984000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr7:98977800-98984200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr7:98978000-98979600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr7:98978000-98979800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:98978000-98979800	Genic enhancers	Fetal Muscle Leg	muscle
26	chr7:98978000-98984200	Weak transcription	HSMMtube	muscle
27	chr7:98978000-98987000	Weak transcription	Small Intestine	intestine
28	chr7:98978200-98979600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr7:98978200-98979600	Strong transcription	Fetal Stomach	stomach
30	chr7:98978200-98979600	Genic enhancers	Lung	lung
31	chr7:98978200-98979600	Genic enhancers	Pancreas	Pancrea
32	chr7:98978200-98979800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr7:98978200-98979800	Flanking Active TSS	HepG2	liver
34	chr7:98978200-98980400	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr7:98978200-98984000	Weak transcription	Fetal Lung	lung
36	chr7:98978200-98984200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr7:98978200-98989800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr7:98978400-98983200	Weak transcription	Fetal Intestine Large	intestine
39	chr7:98978400-98984000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr7:98978400-98984200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr7:98978400-98984200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr7:98978600-98979600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr7:98978600-98979800	Enhancers	Liver	Liver
44	chr7:98978600-98983600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr7:98978600-98984400	Weak transcription	NH-A	brain
46	chr7:98978800-98979600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr7:98978800-98979800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr7:98978800-98979800	Genic enhancers	Placenta	Placenta
49	chr7:98978800-98985000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr7:98978800-98989000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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