Variant report

Variant	rs11054732
Chromosome Location	chr12:12377516-12377517
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	RUNX3	chr12:12377159-12377545	GM12878	blood:	n/a	n/a
2	BHLHE40	chr12:12377214-12377576	GM12878	blood:	n/a	n/a
3	GATA1	chr12:12377113-12377637	PBDE	blood:	n/a	chr12:12377330-12377339 chr12:12377199-12377209
4	GATA3	chr12:12377008-12377549	SK-N-SH	brain:	n/a	chr12:12377330-12377339 chr12:12377199-12377209
5	MEF2A	chr12:12377197-12377695	GM12878	blood:	n/a	chr12:12377461-12377472 chr12:12377604-12377613 chr12:12377601-12377616 chr12:12377600-12377616
6	TCF12	chr12:12377022-12377658	SK-N-SH	brain:	n/a	n/a
7	JUND	chr12:12377220-12377557	GM12878	blood:	n/a	chr12:12377403-12377415
8	RUNX3	chr12:12377138-12377545	GM12878	blood:	n/a	n/a
9	MTA3	chr12:12377200-12377643	GM12878	blood:	n/a	n/a
10	NFIC	chr12:12377157-12377773	GM12878	blood:	n/a	n/a
11	EP300	chr12:12377222-12377529	K562	blood:	n/a	chr12:12377482-12377496
12	BATF	chr12:12377170-12377567	GM12878	blood:	n/a	chr12:12377379-12377390
13	ZNF384	chr12:12377203-12377546	GM12878	blood:	n/a	n/a
14	PML	chr12:12377165-12377527	K562	blood:	n/a	n/a
15	ZNF384	chr12:12377155-12377547	K562	blood:	n/a	n/a
16	ATF2	chr12:12377175-12377535	GM12878	blood:	n/a	n/a
17	FOXM1	chr12:12377207-12377596	GM12878	blood:	n/a	n/a
18	EP300	chr12:12377248-12377625	GM12878	blood:	n/a	chr12:12377582-12377596 chr12:12377482-12377496
19	IRF4	chr12:12377241-12377610	GM12878	blood:	n/a	n/a
20	TAL1	chr12:12377142-12377817	K562	blood:	n/a	n/a
21	EP300	chr12:12377241-12377541	GM12878	blood:	n/a	chr12:12377482-12377496
22	TCF12	chr12:12376972-12377639	SK-N-SH	brain:	n/a	n/a
23	ATF2	chr12:12377116-12377664	GM12878	blood:	n/a	n/a
24	ARID3A	chr12:12377289-12377680	K562	blood:	n/a	n/a
25	EP300	chr12:12377213-12377654	GM12878	blood:	n/a	chr12:12377582-12377596 chr12:12377482-12377496
26	TBL1XR1	chr12:12377195-12377517	K562	blood:	n/a	n/a
27	GATA1	chr12:12376977-12377676	K562	blood:	n/a	chr12:12377330-12377339 chr12:12377199-12377209
28	PML	chr12:12377094-12377546	K562	blood:	n/a	n/a
29	TEAD4	chr12:12377103-12377576	K562	blood:	n/a	n/a
30	NFIC	chr12:12377210-12377578	GM12878	blood:	n/a	n/a
31	GATA3	chr12:12377010-12377657	SK-N-SH	brain:	n/a	chr12:12377330-12377339 chr12:12377199-12377209
32	CEBPD	chr12:12377232-12377534	K562	blood:	n/a	n/a
33	TEAD4	chr12:12377106-12377571	K562	blood:	n/a	n/a
34	JUN	chr12:12377160-12377682	K562	blood:	n/a	chr12:12377403-12377415
35	MEF2A	chr12:12377242-12377625	GM12878	blood:	n/a	chr12:12377461-12377472 chr12:12377604-12377613 chr12:12377601-12377616 chr12:12377600-12377616
36	GATA2	chr12:12377174-12377552	K562	blood:	n/a	chr12:12377330-12377339 chr12:12377199-12377209

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12373050..12374895-chr12:12377294..12378845,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-545P	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10082834	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10083170	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466849	1.00[CHB][hapmap]
rs10845497	0.94[EUR][1000 genomes]
rs10845499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845500	0.85[EUR][1000 genomes]
rs11054702	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11054705	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11054707	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11054709	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs11054710	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs11054713	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs11054720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054746	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs11054765	1.00[CHB][hapmap]
rs11054767	1.00[JPT][hapmap]
rs11829211	0.85[EUR][1000 genomes]
rs12296239	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs12297598	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304957	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307111	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12309246	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12309338	1.00[JPT][hapmap]
rs12310020	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs12311922	0.94[EUR][1000 genomes]
rs12316043	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs12319942	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422312	1.00[CHB][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap]
rs12425185	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12425699	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12425946	1.00[CHB][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap]
rs12427198	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13377971	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs16907789	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs28448423	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56998126	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57055264	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58682800	0.92[EUR][1000 genomes]
rs7308022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311064	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74061123	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061145	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960716	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973583	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973718	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978064	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979919	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9630266	1.00[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv832332	chr12:12344027-12484966	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11054732	LRP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12336200-12381000	Weak transcription	Pancreas	Pancrea
2	chr12:12368200-12379000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr12:12368200-12381400	Weak transcription	Gastric	stomach
4	chr12:12368200-12384200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:12368400-12417200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:12368600-12381000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:12368600-12381400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:12370600-12380800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:12370600-12381000	Weak transcription	Left Ventricle	heart
10	chr12:12370800-12379000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:12370800-12380800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:12370800-12392200	Weak transcription	Brain Substantia Nigra	brain
13	chr12:12371800-12378200	Weak transcription	Fetal Muscle Leg	muscle
14	chr12:12373000-12380800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:12373000-12381200	Weak transcription	Lung	lung
16	chr12:12374000-12377800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:12374600-12381000	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:12374600-12381400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:12374800-12380600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:12374800-12380600	Weak transcription	Brain Angular Gyrus	brain
21	chr12:12374800-12380800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr12:12374800-12383200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:12375000-12378200	Weak transcription	Fetal Intestine Large	intestine
24	chr12:12375000-12379200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr12:12375000-12380800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr12:12375200-12379200	Weak transcription	Liver	Liver
27	chr12:12375200-12379400	Weak transcription	Fetal Kidney	kidney
28	chr12:12375800-12379000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:12376200-12377800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:12376200-12377800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:12376200-12378400	Enhancers	GM12878-XiMat	blood
32	chr12:12376600-12377800	Enhancers	K562	blood
33	chr12:12376600-12378200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:12376800-12377800	Enhancers	NH-A	brain
35	chr12:12376800-12377800	Enhancers	Osteobl	bone
36	chr12:12376800-12378400	Enhancers	NHLF	lung
37	chr12:12376800-12380000	Enhancers	HepG2	liver
38	chr12:12377000-12377800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:12377000-12377800	Enhancers	NHDF-Ad	bronchial
40	chr12:12377200-12377800	Enhancers	A549	lung
41	chr12:12377200-12378800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:12377200-12378800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:12377200-12381000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr12:12377200-12381200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:12377400-12377800	Weak transcription	Fetal Stomach	stomach
46	chr12:12377400-12382400	Weak transcription	HSMM	muscle

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