Variant report

Variant	rs1709116
Chromosome Location	chr19:41672967-41672968
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	ZEB1	chr19:41672745-41673482	HepG2	liver:	n/a	n/a
2	MAFK	chr19:41672886-41673015	HepG2	liver:	n/a	n/a
3	NFIC	chr19:41672859-41673433	HepG2	liver:	n/a	n/a
4	FOXA1	chr19:41672887-41673495	HepG2	liver:	n/a	n/a
5	HDAC2	chr19:41672845-41673402	HepG2	liver:	n/a	n/a
6	FOXA1	chr19:41672883-41673406	HepG2	liver:	n/a	n/a
7	SP1	chr19:41672964-41673471	HepG2	liver:	n/a	n/a
8	MYBL2	chr19:41672829-41673382	HepG2	liver:	n/a	n/a
9	MAX	chr19:41672891-41673535	HepG2	liver:	n/a	n/a
10	FOXA2	chr19:41672731-41673655	HepG2	liver:	n/a	n/a
11	TEAD4	chr19:41672712-41673399	HepG2	liver:	n/a	n/a
12	FOXA1	chr19:41672886-41673444	HepG2	liver:	n/a	n/a
13	ARID3A	chr19:41672807-41673485	HepG2	liver:	n/a	n/a
14	HNF4A	chr19:41672953-41673455	HepG2	liver:	n/a	chr19:41673230-41673248 chr19:41673231-41673246
15	EP300	chr19:41672891-41673409	HepG2	liver:	n/a	n/a
16	FOXA1	chr19:41672928-41673367	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
RPL36P16	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11671185	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1645685	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1645686	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1709124	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1709125	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2432221	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458634	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs305954	0.80[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs305955	0.84[ASN][1000 genomes]
rs305956	0.84[ASN][1000 genomes]
rs305960	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs305961	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs305962	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3391909	chr19:41632754-41688263	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv911767	chr19:41649516-41716271	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41662600-41678200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr19:41664200-41675600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:41665400-41673000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:41665400-41678200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr19:41665400-41678400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:41665400-41678400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr19:41665400-41678600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr19:41665800-41679000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:41666000-41681800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:41666400-41673400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr19:41666400-41678400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr19:41671000-41674000	Enhancers	Fetal Intestine Large	intestine
13	chr19:41671200-41673000	Enhancers	Duodenum Mucosa	Duodenum
14	chr19:41671200-41675200	Enhancers	Stomach Mucosa	stomach
15	chr19:41671400-41675400	Weak transcription	Fetal Stomach	stomach
16	chr19:41671800-41673000	Enhancers	Colonic Mucosa	Colon
17	chr19:41671800-41674000	Enhancers	Fetal Intestine Small	intestine
18	chr19:41671800-41678400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr19:41672000-41679000	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr19:41672000-41680800	Weak transcription	Hela-S3	cervix
21	chr19:41672600-41673200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr19:41672600-41673400	Flanking Active TSS	HepG2	liver
23	chr19:41672800-41673000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr19:41672800-41673000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr19:41672800-41673800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
26	chr19:41672800-41673800	Enhancers	Gastric	stomach
27	chr19:41672800-41673800	Enhancers	Pancreas	Pancrea
28	chr19:41672800-41673800	Enhancers	A549	lung

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