Variant report

Variant	rs188478315
Chromosome Location	chr12:50356533-50356534
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	TCF12	chr12:50356353-50357527	ECC-1	luminal epithelium:	n/a	chr12:50356770-50356780
2	EP300	chr12:50356292-50357440	ECC-1	luminal epithelium:	n/a	n/a
3	SMC3	chr12:50356482-50357176	Hela-S3	cervix:	n/a	n/a
4	SMARCC1	chr12:50356496-50357432	Hela-S3	cervix:	n/a	n/a
5	ZBTB7A	chr12:50355999-50357366	ECC-1	luminal epithelium:	n/a	n/a
6	YY1	chr12:50356392-50357211	ECC-1	luminal epithelium:	n/a	n/a
7	JUND	chr12:50356520-50357162	SK-N-SH	brain:	n/a	chr12:50356859-50356867 chr12:50356857-50356869 chr12:50356858-50356868
8	MAX	chr12:50356357-50357530	MCF-7	breast:	n/a	n/a
9	JUND	chr12:50356470-50357252	MCF-7	breast:	n/a	chr12:50356859-50356867 chr12:50356857-50356869 chr12:50356858-50356868
10	TCF12	chr12:50356483-50357303	A549	lung:	n/a	chr12:50356770-50356780
11	ESR1	chr12:50356344-50357074	ECC-1	luminal epithelium:	n/a	n/a
12	GATA3	chr12:50356509-50357264	SK-N-SH	brain:	n/a	chr12:50356857-50356866 chr12:50356947-50356955
13	YY1	chr12:50356391-50357175	ECC-1	luminal epithelium:	n/a	n/a
14	NFIC	chr12:50356383-50357666	ECC-1	luminal epithelium:	n/a	n/a
15	MAX	chr12:50356369-50357438	ECC-1	luminal epithelium:	n/a	n/a
16	TCF12	chr12:50356454-50357356	SK-N-SH	brain:	n/a	chr12:50356770-50356780
17	NR2F2	chr12:50356515-50357369	MCF-7	breast:	n/a	n/a
18	FOSL2	chr12:50356526-50357230	A549	lung:	n/a	chr12:50356859-50356867 chr12:50356857-50356869 chr12:50356858-50356868
19	EP300	chr12:50356524-50357248	SK-N-SH	brain:	n/a	n/a
20	MAX	chr12:50356384-50357367	A549	lung:	n/a	n/a
21	TCF12	chr12:50356470-50357195	SK-N-SH	brain:	n/a	chr12:50356770-50356780
22	ESR1	chr12:50356400-50357069	ECC-1	luminal epithelium:	n/a	n/a
23	SMARCB1	chr12:50356426-50357470	Hela-S3	cervix:	n/a	n/a
24	ZBTB7A	chr12:50355912-50357521	ECC-1	luminal epithelium:	n/a	n/a
25	NFIC	chr12:50356499-50357413	SK-N-SH	brain:	n/a	n/a
26	GATA3	chr12:50356460-50357311	SK-N-SH	brain:	n/a	chr12:50356857-50356866 chr12:50356947-50356955 chr12:50357259-50357268
27	NFIC	chr12:50356211-50357567	ECC-1	luminal epithelium:	n/a	n/a
28	PBX3	chr12:50356518-50357216	SK-N-SH	brain:	n/a	n/a
29	TEAD4	chr12:50356270-50357495	ECC-1	luminal epithelium:	n/a	n/a
30	FOXA2	chr12:50356530-50357165	A549	lung:	n/a	n/a
31	FOSL2	chr12:50356520-50357223	SK-N-SH	brain:	n/a	chr12:50356859-50356867 chr12:50356857-50356869 chr12:50356858-50356868
32	JUND	chr12:50356525-50357280	SK-N-SH	brain:	n/a	chr12:50356859-50356867 chr12:50356857-50356869 chr12:50356858-50356868
33	PBX3	chr12:50356499-50357253	SK-N-SH	brain:	n/a	n/a
34	ESR1	chr12:50356330-50357135	ECC-1	luminal epithelium:	n/a	n/a
35	ESR1	chr12:50356364-50357175	ECC-1	luminal epithelium:	n/a	n/a
36	MAZ	chr12:50356457-50357101	Hela-S3	cervix:	n/a	n/a
37	MAX	chr12:50356294-50357396	ECC-1	luminal epithelium:	n/a	n/a
38	TCF12	chr12:50356401-50357360	ECC-1	luminal epithelium:	n/a	chr12:50356770-50356780
39	CTCF	chr12:50356420-50356570	Hela-S3	cervix:	n/a	n/a
40	TEAD4	chr12:50356427-50357248	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50353765..50356841-chr12:50356981..50360242,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RACGAP1-1	chr12:50356450-50356566	ENSG00000257588.1
2	lnc-RACGAP1-1	chr12:50356450-50356707	ENSG00000257588.1

Variant related genes	Relation type
AQP6	TF binding region
AQP5	TF binding region
ENSG00000161798	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv558835	chr12:50275137-50433234	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv899072	chr12:50326176-50379667	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899073	chr12:50335628-50360461	Bivalent Enhancer 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	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv899074	chr12:50344976-50360461	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	esv1828759	chr12:50349765-50366300	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	esv1827130	chr12:50349765-50379667	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
14	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer 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	28 gene(s)	inside rSNPs	diseases
15	nsv523899	chr12:50354437-50366300	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv558838	chr12:50355329-50358054	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	nsv558839	chr12:50355381-50358468	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50353000-50357400	Enhancers	HMEC	breast
2	chr12:50353400-50357400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:50353600-50357200	Bivalent Enhancer	Fetal Intestine Small	intestine
4	chr12:50353600-50358400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr12:50354800-50357000	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr12:50355400-50357200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr12:50355400-50357600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr12:50355400-50357800	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr12:50355400-50358200	Enhancers	Pancreas	Pancrea
10	chr12:50355400-50361200	Weak transcription	Lung	lung
11	chr12:50355600-50357400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:50355600-50357400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:50355600-50357400	Enhancers	Brain Cingulate Gyrus	brain
14	chr12:50355600-50357600	Enhancers	Left Ventricle	heart
15	chr12:50355800-50356600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:50355800-50357400	Enhancers	Right Ventricle	heart
17	chr12:50356000-50356600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
18	chr12:50356000-50356800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:50356000-50356800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:50356000-50357000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:50356000-50357000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:50356000-50357000	Enhancers	Brain Substantia Nigra	brain
23	chr12:50356000-50357000	Weak transcription	Right Atrium	heart
24	chr12:50356000-50357400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:50356000-50357400	Bivalent Enhancer	Brain Germinal Matrix	brain
26	chr12:50356000-50357800	Enhancers	Gastric	stomach
27	chr12:50356000-50361000	Weak transcription	Ovary	ovary
28	chr12:50356200-50356800	Enhancers	Brain Anterior Caudate	brain
29	chr12:50356200-50357400	Enhancers	Spleen	Spleen
30	chr12:50356200-50357400	Enhancers	HSMMtube	muscle
31	chr12:50356200-50357800	Enhancers	A549	lung
32	chr12:50356400-50356600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:50356400-50356600	Flanking Active TSS	Esophagus	oesophagus
34	chr12:50356400-50356800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:50356400-50356800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
36	chr12:50356400-50356800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:50356400-50356800	Enhancers	Brain Angular Gyrus	brain
38	chr12:50356400-50356800	Enhancers	HepG2	liver
39	chr12:50356400-50357000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:50356400-50357000	Bivalent Enhancer	Fetal Brain Male	brain
41	chr12:50356400-50357000	Enhancers	Fetal Brain Female	brain
42	chr12:50356400-50357200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:50356400-50357200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
44	chr12:50356400-50357200	Bivalent Enhancer	Fetal Stomach	stomach
45	chr12:50356400-50357200	Bivalent Enhancer	NHEK	skin
46	chr12:50356400-50357400	Enhancers	Brain Hippocampus Middle	brain
47	chr12:50356400-50357400	Enhancers	Fetal Heart	heart
48	chr12:50356400-50357400	Flanking Active TSS	Hela-S3	cervix
49	chr12:50356400-50357400	Enhancers	HSMM	muscle
50	chr12:50356400-50357400	Enhancers	HUVEC	blood vessel

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