Variant report

Variant	rs1982048
Chromosome Location	chr9:116842496-116842497
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	MYBL2	chr9:116842304-116845289	HepG2	liver:	n/a	n/a
2	SP1	chr9:116842406-116845227	A549	lung:	n/a	chr9:116844352-116844366 chr9:116843251-116843260
3	TCF12	chr9:116842319-116845308	A549	lung:	n/a	chr9:116843446-116843456
4	POLR2A	chr9:116842289-116844808	HepG2	liver:	n/a	n/a
5	POLR2A	chr9:116842309-116843002	HepG2	liver:	n/a	n/a
6	REST	chr9:116842485-116845193	A549	lung:	n/a	n/a
7	EP300	chr9:116842281-116844185	A549	lung:	n/a	chr9:116843339-116843349
8	ATF3	chr9:116842433-116843590	A549	lung:	n/a	n/a
9	SP1	chr9:116842368-116845209	A549	lung:	n/a	chr9:116844352-116844366 chr9:116843251-116843260
10	POLR2A	chr9:116842272-116845223	HepG2	liver:	n/a	n/a
11	MAX	chr9:116842190-116845354	HepG2	liver:	n/a	chr9:116843452-116843462 chr9:116844878-116844888
12	FOSL2	chr9:116842296-116844109	A549	lung:	n/a	n/a
13	EP300	chr9:116842411-116844005	A549	lung:	n/a	chr9:116843339-116843349
14	GATA3	chr9:116842475-116843922	A549	lung:	n/a	chr9:116843272-116843282
15	NFIC	chr9:116842323-116845215	HepG2	liver:	n/a	n/a
16	BCL3	chr9:116842282-116843923	A549	lung:	n/a	chr9:116843045-116843054 chr9:116843046-116843055
17	RCOR1	chr9:116842382-116842814	HepG2	liver:	n/a	n/a
18	POLR2A	chr9:116842401-116845170	HepG2	liver:	n/a	n/a
19	MBD4	chr9:116842397-116843842	HepG2	liver:	n/a	n/a
20	POLR2A	chr9:116842329-116845543	HepG2	liver:	n/a	n/a
21	TEAD4	chr9:116842438-116845262	HepG2	liver:	n/a	n/a
22	SIX5	chr9:116842284-116843620	A549	lung:	n/a	n/a
23	NFIC	chr9:116842438-116844070	HepG2	liver:	n/a	n/a
24	MAX	chr9:116842352-116845390	A549	lung:	n/a	chr9:116843452-116843462 chr9:116844878-116844888
25	HEY1	chr9:116842309-116845278	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:116837232..116841114-chr9:116841892..116845820,4	MCF-7	breast:
2	chr9:116841868..116844591-chr9:116846288..116849534,3	MCF-7	breast:
3	chr9:116836243..116838411-chr9:116841082..116842914,2	MCF-7	breast:

Variant related genes	Relation type
AMBP	TF binding region
ENSG00000106927	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10116075	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10119159	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759681	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10982059	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12553054	0.81[JPT][hapmap]
rs1982049	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2093785	0.81[CEU][hapmap]
rs2116403	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2251680	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2285055	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2761691	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478062	0.81[CEU][hapmap]
rs7040719	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7853169	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	esv2422396	chr9:116792944-117354862	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
3	nsv466514	chr9:116810890-116867054	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv615222	chr9:116810890-116867054	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	esv2422492	chr9:116811294-117366643	Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
6	esv2761285	chr9:116811897-117103268	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
7	nsv466515	chr9:116814661-116867054	Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription 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	4 gene(s)	inside rSNPs	diseases
8	nsv615223	chr9:116814661-116867054	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv528822	chr9:116815777-116867054	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking 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 lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv466516	chr9:116815777-116867054	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv466518	chr9:116815777-116867054	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv466519	chr9:116815777-116867054	Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
13	nsv466520	chr9:116815777-116867054	Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
14	nsv466521	chr9:116815777-116867054	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
15	nsv466522	chr9:116815777-116867054	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
16	nsv466523	chr9:116815777-116867054	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
17	nsv471319	chr9:116815777-116867054	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
18	nsv615224	chr9:116815777-116867054	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
19	nsv466524	chr9:116826842-116867054	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv466525	chr9:116826842-116867054	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	nsv615225	chr9:116826842-116867054	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	esv996359	chr9:116839001-116847886	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1982048	KIAA0368	cis	parietal	SCAN
rs1982048	TNFSF8	cis	cerebellum	SCAN
rs1982048	TXNDC8	cis	cerebellum	SCAN
rs1982048	DEC1	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116839000-116845200	Enhancers	Stomach Mucosa	stomach
2	chr9:116839800-116846200	Enhancers	Fetal Intestine Small	intestine
3	chr9:116840000-116847000	Enhancers	Fetal Intestine Large	intestine
4	chr9:116840800-116842800	Weak transcription	Fetal Lung	lung
5	chr9:116840800-116844600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr9:116840800-116845200	Enhancers	Pancreas	Pancrea
7	chr9:116841200-116843600	Weak transcription	Lung	lung
8	chr9:116841400-116842600	Enhancers	Small Intestine	intestine
9	chr9:116841400-116843000	Weak transcription	Colonic Mucosa	Colon
10	chr9:116841600-116842600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr9:116841600-116845200	Enhancers	Fetal Kidney	kidney
12	chr9:116841800-116842600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:116842000-116842800	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr9:116842400-116843000	Flanking Active TSS	A549	lung
15	chr9:116842400-116843200	Flanking Active TSS	HepG2	liver
16	chr9:116842400-116844800	Enhancers	Gastric	stomach
17	chr9:116842400-116844800	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr9:116842400-116845200	Flanking Active TSS	Liver	Liver
19	chr9:116842400-116845200	Enhancers	Duodenum Mucosa	Duodenum

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