Variant report

Variant	rs296764
Chromosome Location	chr12:50364756-50364757
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	CTCF	chr12:50364620-50364770	GM06990	blood:	n/a	n/a
2	CTCF	chr12:50364443-50364799	K562	blood:	n/a	n/a
3	CTCF	chr12:50364450-50364758	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50364552..50366363-chr12:50449249..50451559,2	MCF-7	breast:
2	chr12:50356730..50360184-chr12:50363549..50366213,4	MCF-7	breast:
3	chr12:50154851..50157744-chr12:50364443..50366192,2	K562	blood:

Variant related genes	Relation type
AQP6	TF binding region
ENSG00000161798	Chromatin interaction
ENSG00000110881	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11169179	1.00[EUR][1000 genomes]
rs11169181	1.00[EUR][1000 genomes]
rs12316969	1.00[EUR][1000 genomes]
rs12318294	1.00[EUR][1000 genomes]
rs2697111	1.00[EUR][1000 genomes]
rs296738	1.00[EUR][1000 genomes]
rs296748	1.00[EUR][1000 genomes]
rs296749	1.00[EUR][1000 genomes]
rs296753	1.00[EUR][1000 genomes]
rs296755	1.00[EUR][1000 genomes]
rs296757	1.00[EUR][1000 genomes]
rs296758	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs296761	1.00[EUR][1000 genomes]
rs296765	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372753	1.00[EUR][1000 genomes]
rs425726	1.00[EUR][1000 genomes]
rs455037	1.00[EUR][1000 genomes]
rs60009415	1.00[EUR][1000 genomes]
rs672697	1.00[EUR][1000 genomes]
rs73310966	1.00[EUR][1000 genomes]
rs74087196	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
9	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
10	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
11	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
12	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
13	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

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50357800-50366400	Weak transcription	Gastric	stomach
2	chr12:50361400-50365000	Weak transcription	Hela-S3	cervix
3	chr12:50361400-50372800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:50361600-50368200	Weak transcription	Right Atrium	heart
5	chr12:50361800-50364800	Enhancers	Brain Cingulate Gyrus	brain
6	chr12:50361800-50365200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:50361800-50365800	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr12:50361800-50366200	Enhancers	Brain Substantia Nigra	brain
9	chr12:50361800-50367800	Enhancers	Brain Hippocampus Middle	brain
10	chr12:50362000-50367000	Enhancers	Brain Anterior Caudate	brain
11	chr12:50362000-50371200	Weak transcription	Fetal Brain Female	brain
12	chr12:50362400-50367400	Weak transcription	Brain Germinal Matrix	brain
13	chr12:50362600-50366600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:50362600-50385800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:50363200-50368200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:50364000-50365400	Weak transcription	Brain Angular Gyrus	brain
17	chr12:50364000-50366600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:50364000-50368600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:50364200-50367200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:50364200-50371000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:50364400-50365600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr12:50364400-50366600	Enhancers	NHEK	skin
23	chr12:50364600-50364800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:50364600-50364800	Enhancers	Esophagus	oesophagus
25	chr12:50364600-50365000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:50364600-50365200	Enhancers	A549	lung
27	chr12:50364600-50366200	Enhancers	HMEC	breast

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