Variant report

Variant	rs11054942
Chromosome Location	chr12:12659267-12659268
allele	C/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	BCLAF1	chr12:12658755-12659339	GM12878	blood:	n/a	n/a
2	CREB1	chr12:12658898-12659377	GM12878	blood:	n/a	n/a
3	TEAD4	chr12:12658693-12659622	SK-N-SH	brain:	n/a	n/a
4	BCL11A	chr12:12658764-12659281	GM12878	blood:	n/a	n/a
5	CHD2	chr12:12658815-12659409	GM12878	blood:	n/a	n/a
6	RELA	chr12:12658761-12659368	GM10847	blood:	n/a	n/a
7	WRNIP1	chr12:12658867-12659373	GM12878	blood:	n/a	n/a
8	EP300	chr12:12658292-12660593	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr12:12658327-12660010	SK-N-SH	brain:	n/a	chr12:12659276-12659283 chr12:12659276-12659285 chr12:12659276-12659283 chr12:12659274-12659286 chr12:12659275-12659285 chr12:12659276-12659283 chr12:12659277-12659294 chr12:12659272-12659288 chr12:12659387-12659403 chr12:12659276-12659285
10	RCOR1	chr12:12658832-12659644	K562	blood:	n/a	n/a
11	NFIC	chr12:12658599-12659360	GM12878	blood:	n/a	n/a
12	TCF12	chr12:12658487-12660034	SK-N-SH	brain:	n/a	chr12:12659784-12659793
13	TBL1XR1	chr12:12658515-12659353	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:12658804-12659403	GM12891	blood:	n/a	n/a
15	NFIC	chr12:12658493-12659349	GM12878	blood:	n/a	n/a
16	EBF1	chr12:12658841-12659286	GM12878	blood:	n/a	n/a
17	BHLHE40	chr12:12658781-12659344	GM12878	blood:	n/a	n/a
18	RCOR1	chr12:12658780-12659355	GM12878	blood:	n/a	n/a
19	TBP	chr12:12658533-12659381	GM12878	blood:	n/a	n/a
20	PBX3	chr12:12658594-12659438	SK-N-SH	brain:	n/a	n/a
21	MAX	chr12:12658717-12659288	SK-N-SH	brain:	n/a	n/a
22	GATA3	chr12:12658514-12659952	SK-N-SH	brain:	n/a	chr12:12659276-12659283 chr12:12659276-12659285 chr12:12659276-12659283 chr12:12659274-12659286 chr12:12659275-12659285 chr12:12659276-12659283 chr12:12659277-12659294 chr12:12659272-12659288 chr12:12659387-12659403 chr12:12659276-12659285
23	TEAD4	chr12:12658647-12659441	SK-N-SH	brain:	n/a	n/a
24	SMC3	chr12:12658845-12659447	GM12878	blood:	n/a	n/a
25	EP300	chr12:12658885-12659479	K562	blood:	n/a	n/a
26	PML	chr12:12658723-12659445	GM12878	blood:	n/a	n/a
27	NFATC1	chr12:12658683-12659501	GM12878	blood:	n/a	n/a
28	FOSL2	chr12:12658694-12659438	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr12:12658738-12659923	PFSK-1	brain:	n/a	n/a
30	JUND	chr12:12658612-12659456	K562	blood:	n/a	n/a
31	ATF2	chr12:12658632-12659411	GM12878	blood:	n/a	n/a
32	EP300	chr12:12658686-12659542	SK-N-SH_RA	brain:	n/a	n/a
33	SIN3AK20	chr12:12658796-12659305	PFSK-1	brain:	n/a	n/a
34	RUNX3	chr12:12658711-12659326	GM12878	blood:	n/a	n/a
35	POLR2A	chr12:12658177-12659392	GM12878	blood:	n/a	n/a
36	IKZF1	chr12:12658711-12659593	GM12878	blood:	n/a	n/a
37	NFIC	chr12:12658630-12659807	SK-N-SH	brain:	n/a	n/a
38	MEF2A	chr12:12658670-12659404	SK-N-SH	brain:	n/a	n/a
39	POU2F2	chr12:12658762-12659477	GM12891	blood:	n/a	chr12:12658813-12658835 chr12:12659060-12659075
40	IRF1	chr12:12658879-12659377	K562	blood:	n/a	chr12:12659051-12659065 chr12:12659052-12659063 chr12:12659052-12659065 chr12:12659051-12659065
41	POLR2A	chr12:12658756-12659399	GM12878	blood:	n/a	n/a
42	REST	chr12:12658746-12659324	PFSK-1	brain:	n/a	n/a
43	CUX1	chr12:12658836-12659470	GM12878	blood:	n/a	n/a
44	MTA3	chr12:12658696-12659462	GM12878	blood:	n/a	n/a
45	ATF2	chr12:12658677-12659341	GM12878	blood:	n/a	n/a
46	RELA	chr12:12658757-12659314	GM19099	blood:	n/a	n/a
47	STAT3	chr12:12658817-12659353	GM12878	blood:	n/a	n/a
48	CHD1	chr12:12658494-12659389	GM12878	blood:	n/a	n/a
49	NFATC1	chr12:12658633-12659335	GM12878	blood:	n/a	n/a
50	RAD21	chr12:12658802-12659330	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12659166..12661033-chr12:12690816..12693581,2	MCF-7	breast:
2	chr12:12657878..12659784-chr12:12714344..12718404,3	K562	blood:

Variant related genes	Relation type
DUSP16	TF binding region
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10743988	0.94[ASN][1000 genomes]
rs10772570	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10845552	0.86[CHB][hapmap];0.91[MEX][hapmap]
rs10845559	0.83[ASW][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.93[ASN][1000 genomes]
rs10845560	0.88[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.95[ASN][1000 genomes]
rs10845563	0.81[GIH][hapmap]
rs10845567	0.94[CHB][hapmap];0.94[ASN][1000 genomes]
rs10845568	0.92[CEU][hapmap]
rs10845572	0.94[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11054937	0.95[ASN][1000 genomes]
rs11054940	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054941	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.95[ASN][1000 genomes]
rs11054947	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11613385	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12422540	1.00[CHB][hapmap];0.80[JPT][hapmap];0.93[ASN][1000 genomes]
rs1558822	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041927	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2111271	0.90[CHB][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs2417190	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3815591	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4255620	0.95[ASN][1000 genomes]
rs4763832	0.89[ASN][1000 genomes]
rs4763833	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7137455	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7294378	0.86[ASN][1000 genomes]
rs7295305	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7295427	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7308097	0.92[LWK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs7310652	0.95[ASN][1000 genomes]
rs7972902	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs933575	0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.93[ASN][1000 genomes]
rs962928	0.88[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758295	chr12:12620654-12783124	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2759880	chr12:12620654-12783124	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv898811	chr12:12655443-12928295	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12630600-12661200	Weak transcription	NHEK	skin
2	chr12:12630800-12659600	Weak transcription	Esophagus	oesophagus
3	chr12:12630800-12681000	Weak transcription	Colonic Mucosa	Colon
4	chr12:12634400-12685200	Weak transcription	Hela-S3	cervix
5	chr12:12639400-12679600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:12641600-12663600	Weak transcription	Lung	lung
7	chr12:12641600-12686200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:12647000-12661400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:12652800-12665000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:12653800-12669000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:12654000-12661200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:12654200-12660400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr12:12654400-12667200	Weak transcription	Primary T cells from cord blood	blood
14	chr12:12656000-12666400	Weak transcription	Spleen	Spleen
15	chr12:12656600-12660600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:12656800-12670800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:12657200-12659600	Enhancers	HepG2	liver
18	chr12:12657400-12659800	Enhancers	Stomach Mucosa	stomach
19	chr12:12657400-12660400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:12657600-12660400	Enhancers	Fetal Intestine Large	intestine
21	chr12:12657800-12659800	Enhancers	Placenta Amnion	Placenta Amnion
22	chr12:12658000-12659400	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr12:12658000-12660400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:12658000-12660800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:12658000-12660800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:12658200-12659400	Enhancers	Fetal Muscle Leg	muscle
27	chr12:12658200-12659600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr12:12658200-12659800	Enhancers	H1 Cell Line	embryonic stem cell
29	chr12:12658200-12659800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:12658200-12659800	Enhancers	Thymus	Thymus
31	chr12:12658200-12659800	Flanking Active TSS	GM12878-XiMat	blood
32	chr12:12658200-12660000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:12658200-12660000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:12658200-12660400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:12658200-12660400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:12658200-12660400	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr12:12658200-12660400	Enhancers	Placenta	Placenta
38	chr12:12658200-12660400	Enhancers	Fetal Stomach	stomach
39	chr12:12658200-12660400	Enhancers	Right Ventricle	heart
40	chr12:12658200-12660400	Enhancers	Small Intestine	intestine
41	chr12:12658200-12660600	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr12:12658200-12660800	Enhancers	Pancreas	Pancrea
43	chr12:12658200-12661800	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr12:12658200-12662800	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr12:12658400-12659400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:12658400-12659600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr12:12658400-12659800	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr12:12658400-12659800	Flanking Active TSS	Liver	Liver
49	chr12:12658400-12660000	Flanking Active TSS	NHDF-Ad	bronchial
50	chr12:12658400-12660400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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