Variant report

Variant	rs12609306
Chromosome Location	chr19:45315694-45315695
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	POLR2A	chr19:45315688-45315765	HepG2	liver:	n/a	n/a
2	TCF12	chr19:45315640-45315950	HepG2	liver:	n/a	n/a
3	HNF4A	chr19:45315480-45315958	HepG2	liver:	n/a	chr19:45315816-45315831
4	TEAD4	chr19:45315610-45315964	HepG2	liver:	n/a	n/a
5	HDAC2	chr19:45315584-45315986	HepG2	liver:	n/a	n/a
6	MYBL2	chr19:45315510-45316011	HepG2	liver:	n/a	n/a
7	HNF4A	chr19:45315463-45316050	HepG2	liver:	n/a	chr19:45315816-45315831
8	POLR2A	chr19:45315424-45315843	HepG2	liver:	n/a	n/a
9	ZBTB7A	chr19:45315559-45315989	HepG2	liver:	n/a	n/a
10	POLR2A	chr19:45315500-45315771	HepG2	liver:	n/a	n/a
11	ZBTB7A	chr19:45315558-45315952	HepG2	liver:	n/a	n/a
12	HEY1	chr19:45315425-45315882	HepG2	liver:	n/a	n/a
13	RCOR1	chr19:45315680-45315830	HepG2	liver:	n/a	n/a
14	CEBPD	chr19:45315436-45315919	HepG2	liver:	n/a	n/a
15	EP300	chr19:45315470-45316007	HepG2	liver:	n/a	n/a
16	FOXA1	chr19:45315475-45315942	HepG2	liver:	n/a	n/a
17	POLR2A	chr19:45315443-45315910	HepG2	liver:	n/a	n/a
18	HNF4G	chr19:45315445-45316050	HepG2	liver:	n/a	chr19:45315734-45315749
19	MAZ	chr19:45315622-45315861	HepG2	liver:	n/a	n/a
20	HNF4A	chr19:45315574-45316043	HepG2	liver:	n/a	chr19:45315816-45315831
21	HNF4G	chr19:45315548-45315963	HepG2	liver:	n/a	chr19:45315734-45315749
22	EP300	chr19:45315553-45315916	HepG2	liver:	n/a	n/a
23	HDAC2	chr19:45315527-45316016	HepG2	liver:	n/a	n/a
24	EP300	chr19:45315651-45315914	HepG2	liver:	n/a	n/a
25	POLR2A	chr19:45315340-45315998	HepG2	liver:	n/a	n/a
26	SP1	chr19:45315468-45316091	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
BCAM	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs28399603	1.00[ASN][1000 genomes]
rs28399608	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28742260	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3745159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs748913	0.91[ASN][1000 genomes]
rs8101274	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs922387	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912117	chr19:45298069-45322744	Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv912118	chr19:45300056-45326664	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv912119	chr19:45304307-45317089	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv912120	chr19:45304307-45317469	Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv912121	chr19:45304307-45319297	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv912122	chr19:45304307-45324516	Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv579862	chr19:45310319-45316807	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv912124	chr19:45310319-45318564	Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv912125	chr19:45310319-45321841	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	nsv579863	chr19:45310319-45322451	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv912126	chr19:45311523-45317089	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	nsv912127	chr19:45312114-45316807	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	nsv912128	chr19:45312114-45321841	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45313000-45316400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:45313000-45316600	Weak transcription	HUVEC	blood vessel
3	chr19:45313000-45318200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr19:45313000-45319000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr19:45313000-45320400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr19:45313000-45325400	Weak transcription	Brain Hippocampus Middle	brain
7	chr19:45313400-45316400	Weak transcription	NHLF	lung
8	chr19:45313400-45316800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:45313400-45321200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr19:45313400-45321600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr19:45313600-45316600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr19:45313600-45317000	Enhancers	Fetal Heart	heart
13	chr19:45313600-45322800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr19:45313600-45323400	Weak transcription	Colon Smooth Muscle	Colon
15	chr19:45313600-45326400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:45313600-45326600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr19:45313800-45316800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr19:45313800-45316800	Weak transcription	A549	lung
19	chr19:45314000-45316400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr19:45314000-45316400	Weak transcription	Left Ventricle	heart
21	chr19:45314000-45316600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:45314000-45316800	Weak transcription	Fetal Lung	lung
23	chr19:45314000-45316800	Weak transcription	Placenta	Placenta
24	chr19:45314000-45318600	Weak transcription	Fetal Brain Male	brain
25	chr19:45314000-45321200	Weak transcription	Liver	Liver
26	chr19:45314000-45323400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:45314000-45323600	Weak transcription	HSMMtube	muscle
28	chr19:45314200-45315800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr19:45314200-45316400	Weak transcription	Adipose Nuclei	Adipose
30	chr19:45314200-45316400	Weak transcription	Esophagus	oesophagus
31	chr19:45314200-45316800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr19:45314200-45316800	Genic enhancers	Fetal Intestine Small	intestine
33	chr19:45314200-45316800	Weak transcription	Fetal Kidney	kidney
34	chr19:45314200-45319400	Genic enhancers	Fetal Muscle Trunk	muscle
35	chr19:45314200-45323200	Weak transcription	Right Atrium	heart
36	chr19:45314400-45316600	Weak transcription	HMEC	breast
37	chr19:45314400-45316800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr19:45314400-45318000	Strong transcription	Ovary	ovary
39	chr19:45314400-45318600	Strong transcription	Aorta	Aorta
40	chr19:45314400-45319000	Strong transcription	NHEK	skin
41	chr19:45314600-45315800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
42	chr19:45314600-45316800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr19:45314600-45317000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr19:45314600-45318800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:45314600-45319000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:45314600-45319200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr19:45314600-45322200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr19:45314600-45323800	Strong transcription	Fetal Stomach	stomach
49	chr19:45314600-45326200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:45314800-45315800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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