Variant report

Variant	rs11183454
Chromosome Location	chr12:46785587-46785588
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	FOXM1	chr12:46785226-46785927	MCF-7	breast:	n/a	n/a
2	FOS	chr12:46785441-46785692	MCF10A-Er-Src	breast:	n/a	n/a
3	ESR1	chr12:46785417-46785878	T-47D	breast:	n/a	n/a
4	FOXA1	chr12:46785352-46785759	T-47D	breast:	n/a	n/a
5	GATA3	chr12:46785336-46785785	T-47D	breast:	n/a	n/a
6	TCF12	chr12:46785302-46786004	SK-N-SH	brain:	n/a	n/a
7	EBF1	chr12:46785429-46785722	GM12878	blood:	n/a	chr12:46785583-46785594
8	TEAD4	chr12:46785448-46785803	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr12:46785176-46786041	SK-N-SH	brain:	n/a	n/a
10	NFIC	chr12:46785319-46785857	SK-N-SH	brain:	n/a	n/a
11	STAT3	chr12:46785422-46785677	MCF10A-Er-Src	breast:	n/a	chr12:46785655-46785663 chr12:46785485-46785492
12	GATA3	chr12:46785284-46785893	MCF-7	breast:	n/a	n/a
13	FOXA1	chr12:46785440-46785698	T-47D	breast:	n/a	n/a
14	GATA3	chr12:46785377-46785871	T-47D	breast:	n/a	n/a
15	EP300	chr12:46785322-46785878	T-47D	breast:	n/a	n/a
16	GATA3	chr12:46785281-46785959	MCF-7	breast:	n/a	n/a
17	ESR1	chr12:46785390-46785859	T-47D	breast:	n/a	n/a
18	EP300	chr12:46785265-46786039	SK-N-SH	brain:	n/a	n/a
19	EBF1	chr12:46785348-46785790	GM12878	blood:	n/a	chr12:46785583-46785594
20	PBX3	chr12:46785275-46785858	SK-N-SH	brain:	n/a	n/a
21	GATA3	chr12:46785287-46785932	SK-N-SH	brain:	n/a	n/a
22	PBX3	chr12:46785333-46785874	SK-N-SH	brain:	n/a	n/a
23	STAT3	chr12:46785418-46785642	MCF10A-Er-Src	breast:	n/a	chr12:46785485-46785492
24	STAT3	chr12:46785425-46785674	MCF10A-Er-Src	breast:	n/a	chr12:46785655-46785663 chr12:46785485-46785492

No.	Distal block	Cell Line	Cell type
1	chr12:46785191..46787312-chr12:46820790..46822751,2	K562	blood:
2	chr12:46661461..46664528-chr12:46785581..46788536,3	MCF-7	breast:
3	chr12:46784468..46786236-chr20:55203268..55205812,2	MCF-7	breast:
4	chr12:46785131..46787276-chr12:46823023..46825846,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARID2-12	chr12:46782639-46785909	NONHSAT027878

Variant related genes	Relation type
ENSG00000257496	TF binding region
ENSG00000087510	Chromatin interaction
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10467215	0.82[CHB][hapmap]
rs10506267	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs10506268	1.00[EUR][1000 genomes]
rs11183467	0.88[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11183482	0.88[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs11183487	1.00[AMR][1000 genomes]
rs11183500	0.82[CHB][hapmap]
rs11183510	0.82[CHB][hapmap]
rs1125908	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11830769	1.00[EUR][1000 genomes]
rs11834905	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12299499	0.84[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12314541	0.80[YRI][hapmap]
rs12317255	0.88[CHB][hapmap];1.00[AMR][1000 genomes]
rs12320438	1.00[AMR][1000 genomes]
rs12321512	0.94[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12321642	1.00[AMR][1000 genomes]
rs12321960	0.83[CHB][hapmap]
rs12322378	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13377959	0.88[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17096884	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17096896	0.94[CHB][hapmap];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17096922	0.88[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1948425	0.94[JPT][hapmap]
rs2125646	0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes]
rs2307059	0.85[JPT][hapmap]
rs2307062	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2307063	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2408509	0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34280632	1.00[AMR][1000 genomes]
rs35875247	1.00[AMR][1000 genomes]
rs36010856	1.00[AMR][1000 genomes]
rs3742061	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4768118	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs56036156	1.00[AMR][1000 genomes]
rs56196954	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56222195	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56314009	1.00[AMR][1000 genomes]
rs57067899	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57149475	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57271454	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57425661	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58460251	1.00[AMR][1000 genomes]
rs58890669	1.00[AMR][1000 genomes]
rs59608605	1.00[AMR][1000 genomes]
rs60565802	1.00[AMR][1000 genomes]
rs60628240	1.00[EUR][1000 genomes]
rs60878594	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs60977966	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61232019	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61406609	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61517444	1.00[EUR][1000 genomes]
rs73282532	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73282561	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73282591	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73290315	1.00[AMR][1000 genomes]
rs74082254	1.00[AMR][1000 genomes]
rs74083707	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74083710	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74084031	1.00[EUR][1000 genomes]
rs7488027	1.00[AMR][1000 genomes]
rs7953339	0.82[CHB][hapmap]
rs7954314	0.88[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7965618	1.00[AMR][1000 genomes]
rs7967889	0.88[CHB][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes]
rs7977319	1.00[AMR][1000 genomes]
rs7980023	0.82[CHB][hapmap]
rs923788	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9669404	1.00[YRI][hapmap];0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46778400-46786800	Enhancers	NHDF-Ad	bronchial
2	chr12:46778600-46787000	Enhancers	Fetal Lung	lung
3	chr12:46778800-46797200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:46779600-46786000	Weak transcription	Gastric	stomach
5	chr12:46779600-46786400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:46779600-46786400	Weak transcription	Right Ventricle	heart
7	chr12:46779600-46802800	Weak transcription	Pancreas	Pancrea
8	chr12:46780600-46786800	Weak transcription	Brain Substantia Nigra	brain
9	chr12:46780600-46788600	Weak transcription	Fetal Brain Male	brain
10	chr12:46780800-46785600	Enhancers	Liver	Liver
11	chr12:46781000-46785600	Flanking Active TSS	GM12878-XiMat	blood
12	chr12:46781200-46785600	Enhancers	HUVEC	blood vessel
13	chr12:46781400-46786600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:46781400-46787000	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr12:46781400-46787200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:46781600-46789200	Weak transcription	Fetal Stomach	stomach
17	chr12:46781600-46795400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:46781800-46785600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:46781800-46786400	Weak transcription	Colonic Mucosa	Colon
20	chr12:46781800-46786400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr12:46781800-46786400	Weak transcription	Left Ventricle	heart
22	chr12:46781800-46786600	Enhancers	NHLF	lung
23	chr12:46781800-46795000	Weak transcription	Fetal Muscle Leg	muscle
24	chr12:46782000-46787200	Enhancers	Hela-S3	cervix
25	chr12:46782000-46794600	Weak transcription	Fetal Kidney	kidney
26	chr12:46782000-46794600	Weak transcription	Placenta	Placenta
27	chr12:46782000-46794600	Weak transcription	Psoas Muscle	Psoas
28	chr12:46782400-46792600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr12:46782800-46796600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr12:46783000-46786000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:46783000-46786800	Enhancers	Osteobl	bone
32	chr12:46783000-46794200	Weak transcription	Thymus	Thymus
33	chr12:46783200-46786600	Enhancers	Muscle Satellite Cultured Cells	--
34	chr12:46783200-46790800	Weak transcription	Ovary	ovary
35	chr12:46783200-46795600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:46783200-46796200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:46783200-46796600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr12:46783200-46796800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:46783400-46786200	Weak transcription	K562	blood
40	chr12:46783400-46786400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr12:46783400-46786400	Weak transcription	Aorta	Aorta
42	chr12:46783400-46786600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:46783400-46794600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:46783400-46795000	Weak transcription	Fetal Heart	heart
45	chr12:46783400-46795400	Weak transcription	HSMM	muscle
46	chr12:46783400-46796200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:46783600-46786400	Weak transcription	HMEC	breast
48	chr12:46784000-46786600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:46784000-46787000	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr12:46784200-46785600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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