Variant report

Variant	rs12954934
Chromosome Location	chr18:29534459-29534460
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	USF2	chr18:29534407-29534715	HepG2	liver:	n/a	n/a
2	MYC	chr18:29534331-29534623	MCF10A-Er-Src	breast:	n/a	n/a
3	USF1	chr18:29534376-29534791	HCT-116	colon:	n/a	chr18:29534580-29534591 chr18:29534514-29534525
4	USF1	chr18:29534271-29534787	HCT-116	colon:	n/a	chr18:29534580-29534591 chr18:29534514-29534525
5	MYC	chr18:29534328-29534650	MCF10A-Er-Src	breast:	n/a	n/a
6	CHD2	chr18:29534335-29534686	Hela-S3	cervix:	n/a	n/a
7	BHLHE40	chr18:29534377-29534734	HepG2	liver:	n/a	n/a
8	USF1	chr18:29534345-29534663	SK-N-SH_RA	brain:	n/a	chr18:29534580-29534591 chr18:29534514-29534525
9	FOSL2	chr18:29534309-29534619	HepG2	liver:	n/a	chr18:29534548-29534560
10	STAT3	chr18:29534366-29534640	MCF10A-Er-Src	breast:	n/a	n/a
11	REST	chr18:29534420-29534766	PFSK-1	brain:	n/a	n/a
12	STAT3	chr18:29534330-29534701	MCF10A-Er-Src	breast:	n/a	n/a
13	STAT3	chr18:29534335-29534734	MCF10A-Er-Src	breast:	n/a	n/a
14	CEBPB	chr18:29534331-29534696	HepG2	liver:	n/a	chr18:29534509-29534520
15	USF1	chr18:29534436-29534619	HepG2	liver:	n/a	chr18:29534580-29534591 chr18:29534514-29534525
16	FOS	chr18:29534334-29534669	MCF10A-Er-Src	breast:	n/a	chr18:29534548-29534560
17	USF1	chr18:29534399-29534697	SK-N-SH_RA	brain:	n/a	chr18:29534580-29534591 chr18:29534514-29534525
18	MXI1	chr18:29534387-29534689	Hela-S3	cervix:	n/a	n/a
19	TFAP2C	chr18:29534373-29534708	Hela-S3	cervix:	n/a	n/a
20	MAX	chr18:29534382-29534709	Hela-S3	cervix:	n/a	n/a
21	MAX	chr18:29534293-29534785	HCT-116	colon:	n/a	n/a
22	JUND	chr18:29534322-29534673	Hela-S3	cervix:	n/a	chr18:29534548-29534560
23	ARID3A	chr18:29534309-29534712	HepG2	liver:	n/a	n/a
24	FOS	chr18:29534332-29534678	MCF10A-Er-Src	breast:	n/a	chr18:29534548-29534560
25	HNF4A	chr18:29534437-29534663	HepG2	liver:	n/a	chr18:29534519-29534537 chr18:29534520-29534535
26	NFIC	chr18:29534386-29534653	HepG2	liver:	n/a	n/a
27	USF1	chr18:29534404-29534685	HepG2	liver:	n/a	chr18:29534580-29534591 chr18:29534514-29534525
28	EP300	chr18:29534369-29534771	SK-N-SH_RA	brain:	n/a	n/a
29	HDAC2	chr18:29534358-29534677	HepG2	liver:	n/a	n/a
30	RFX5	chr18:29534339-29534690	Hela-S3	cervix:	n/a	n/a
31	STAT3	chr18:29534308-29534706	Hela-S3	cervix:	n/a	n/a
32	SMC3	chr18:29534358-29534685	Hela-S3	cervix:	n/a	n/a
33	MAZ	chr18:29534423-29534705	Hela-S3	cervix:	n/a	n/a
34	CEBPB	chr18:29534329-29534700	HepG2	liver:	n/a	chr18:29534509-29534520
35	CEBPB	chr18:29534279-29534721	Hela-S3	cervix:	n/a	chr18:29534509-29534520
36	HNF4A	chr18:29534368-29534645	HepG2	liver:	n/a	chr18:29534519-29534537 chr18:29534520-29534535
37	EP300	chr18:29534402-29534766	SK-N-SH_RA	brain:	n/a	n/a
38	RCOR1	chr18:29534449-29534528	K562	blood:	n/a	n/a
39	TCF7L2	chr18:29534397-29534664	Hela-S3	cervix:	n/a	n/a
40	CEBPB	chr18:29534379-29534599	HepG2	liver:	n/a	chr18:29534509-29534520
41	USF1	chr18:29534415-29534733	SK-N-SH	brain:	n/a	chr18:29534580-29534591 chr18:29534514-29534525
42	CEBPB	chr18:29534365-29534797	HCT-116	colon:	n/a	chr18:29534509-29534520
43	SP1	chr18:29534323-29534664	HepG2	liver:	n/a	n/a
44	HNF4G	chr18:29534360-29534619	HepG2	liver:	n/a	chr18:29534521-29534536 chr18:29534519-29534537
45	JUND	chr18:29534393-29534654	HepG2	liver:	n/a	chr18:29534548-29534560
46	EP300	chr18:29534320-29534676	Hela-S3	cervix:	n/a	n/a
47	GTF2F1	chr18:29534377-29534674	Hela-S3	cervix:	n/a	n/a
48	RCOR1	chr18:29534330-29534656	Hela-S3	cervix:	n/a	n/a
49	PRDM1	chr18:29534348-29534728	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr18:29534414-29534562	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29522234..29525588-chr18:29534457..29537204,4	MCF-7	breast:

Variant related genes	Relation type
TRAPPC8	TF binding region
ENSG00000153339	Chromatin interaction
ENSG00000263823	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11659714	0.84[EUR][1000 genomes]
rs12326193	0.87[EUR][1000 genomes]
rs12607039	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12965971	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2009538	0.94[ASN][1000 genomes]
rs2048244	0.90[JPT][hapmap]
rs2162378	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2421178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28639693	0.87[EUR][1000 genomes]
rs4344833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4799610	0.96[YRI][hapmap]
rs61736627	0.86[EUR][1000 genomes]
rs62093904	0.86[EUR][1000 genomes]
rs6506952	0.83[YRI][hapmap]
rs7504605	0.94[ASN][1000 genomes]
rs7504671	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8097835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8098465	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs972358	0.94[ASN][1000 genomes]
rs974124	0.94[ASN][1000 genomes]
rs9949272	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9950155	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9950809	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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	nsv1067252	chr18:29475073-29583744	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1065285	chr18:29527884-29614986	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29525600-29537400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr18:29530800-29534600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr18:29531400-29536800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr18:29533400-29534800	Enhancers	Small Intestine	intestine
5	chr18:29533600-29534800	Enhancers	Hela-S3	cervix
6	chr18:29533600-29534800	Enhancers	HepG2	liver
7	chr18:29533600-29535200	Enhancers	Fetal Intestine Small	intestine
8	chr18:29533800-29534800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr18:29533800-29535000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr18:29533800-29535200	Enhancers	Liver	Liver
11	chr18:29534200-29534600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr18:29534200-29534800	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr18:29534400-29534600	Enhancers	Right Atrium	heart
14	chr18:29534400-29534800	Enhancers	H1 Cell Line	embryonic stem cell
15	chr18:29534400-29534800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr18:29534400-29534800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr18:29534400-29534800	Enhancers	Fetal Heart	heart
18	chr18:29534400-29535200	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr18:29534400-29535200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr18:29534400-29537400	Weak transcription	Fetal Intestine Large	intestine

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