Variant report

Variant	rs1886128
Chromosome Location	chr9:116861763-116861764
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	HDAC2	chr9:116861431-116861846	HepG2	liver:	n/a	n/a
2	FOXA1	chr9:116861322-116861871	HepG2	liver:	n/a	n/a
3	MYBL2	chr9:116861393-116861836	HepG2	liver:	n/a	n/a
4	ZBTB7A	chr9:116861646-116861855	HepG2	liver:	n/a	n/a
5	SP1	chr9:116861384-116861940	HepG2	liver:	n/a	chr9:116861669-116861683
6	EP300	chr9:116861425-116861878	HepG2	liver:	n/a	n/a
7	FOXA1	chr9:116861369-116861868	HepG2	liver:	n/a	n/a
8	FOXA2	chr9:116861491-116861814	HepG2	liver:	n/a	n/a
9	FOXA2	chr9:116861494-116861896	A549	lung:	n/a	n/a
10	FOXA1	chr9:116861391-116861924	HepG2	liver:	n/a	n/a
11	YY1	chr9:116861373-116861954	HepG2	liver:	n/a	n/a
12	MAZ	chr9:116861536-116861780	HepG2	liver:	n/a	n/a
13	FOXA1	chr9:116861488-116861830	HepG2	liver:	n/a	n/a
14	POLR2A	chr9:116861232-116862231	HepG2	liver:	n/a	n/a
15	NFIC	chr9:116861521-116861819	HepG2	liver:	n/a	n/a
16	TEAD4	chr9:116861398-116861912	HepG2	liver:	n/a	n/a
17	SP1	chr9:116861460-116861930	A549	lung:	n/a	chr9:116861669-116861683
18	FOXA2	chr9:116861287-116861938	A549	lung:	n/a	n/a
19	TEAD4	chr9:116861290-116861778	ECC-1	luminal epithelium:	n/a	n/a
20	TCF12	chr9:116861337-116862025	A549	lung:	n/a	chr9:116861710-116861720
21	MYC	chr9:116861512-116861765	HepG2	liver:	n/a	n/a
22	HEY1	chr9:116861379-116861991	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
KIF12	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13284299	0.89[ASN][1000 genomes]
rs13285436	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1465657	0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1465659	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1560539	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2093785	0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2251700	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2418265	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs3810929	0.92[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4979338	0.96[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6478062	0.94[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6478063	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6478064	0.88[ASN][1000 genomes]
rs6478065	0.87[ASN][1000 genomes]
rs6478066	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7029198	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7036734	0.94[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs7037166	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7045137	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7853169	0.94[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7854030	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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	nsv870215	chr9:116842614-117070344	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	124 gene(s)	inside rSNPs	diseases
23	nsv893751	chr9:116846467-116874355	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv515856	chr9:116853797-116867054	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	esv3326630	chr9:116859356-116862304	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
26	esv3328680	chr9:116859781-116862229	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1886128	KIAA0368	cis	parietal	SCAN
rs1886128	AMBP	cis	parietal	SCAN
rs1886128	DEC1	cis	parietal	SCAN
rs1886128	KIF12	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116858800-116862200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr9:116859400-116862200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr9:116859600-116861800	Bivalent Enhancer	Placenta	Placenta
4	chr9:116859800-116862400	Enhancers	Spleen	Spleen
5	chr9:116860000-116861800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
6	chr9:116860000-116862000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr9:116860200-116862000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr9:116860800-116862000	Enhancers	Lung	lung
9	chr9:116861000-116861800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:116861000-116862000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
11	chr9:116861200-116861800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
12	chr9:116861200-116861800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr9:116861200-116861800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr9:116861200-116861800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:116861200-116861800	Flanking Active TSS	Liver	Liver
16	chr9:116861200-116861800	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr9:116861200-116861800	Flanking Active TSS	A549	lung
18	chr9:116861200-116862000	Bivalent Enhancer	Fetal Brain Male	brain
19	chr9:116861200-116862000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
20	chr9:116861200-116862600	Flanking Active TSS	HepG2	liver
21	chr9:116861400-116861800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:116861400-116861800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:116861400-116861800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
24	chr9:116861400-116861800	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr9:116861400-116862200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:116861400-116862200	Weak transcription	HUVEC	blood vessel
27	chr9:116861400-116862400	Enhancers	Stomach Mucosa	stomach
28	chr9:116861600-116861800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
29	chr9:116861600-116861800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
30	chr9:116861600-116861800	Enhancers	Colonic Mucosa	Colon
31	chr9:116861600-116861800	Active TSS	Duodenum Mucosa	Duodenum
32	chr9:116861600-116861800	Bivalent Enhancer	Fetal Brain Female	brain
33	chr9:116861600-116861800	Active TSS	Fetal Intestine Large	intestine
34	chr9:116861600-116861800	Active TSS	Fetal Kidney	kidney
35	chr9:116861600-116861800	Enhancers	Fetal Lung	lung
36	chr9:116861600-116862000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
37	chr9:116861600-116862000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
38	chr9:116861600-116862000	Flanking Active TSS	Fetal Intestine Small	intestine
39	chr9:116861600-116862000	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr9:116861600-116862200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr9:116861600-116862600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr9:116861600-116862600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr9:116861600-116862600	Enhancers	Pancreas	Pancrea

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