Variant report

Variant	rs59481807
Chromosome Location	chr12:50362367-50362368
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	BHLHE40	chr12:50362269-50362497	K562	blood:	n/a	n/a
2	USF1	chr12:50362191-50362409	HepG2	liver:	n/a	n/a
3	BHLHE40	chr12:50362156-50362493	HepG2	liver:	n/a	n/a
4	SMC3	chr12:50360284-50362514	SK-N-SH	brain:	n/a	chr12:50360927-50360941 chr12:50361180-50361188 chr12:50361389-50361403
5	CTCF	chr12:50362240-50362390	HRPEpiC	eye:	n/a	n/a
6	RAD21	chr12:50359861-50362422	SK-N-SH	brain:	n/a	chr12:50361388-50361407 chr12:50361632-50361646 chr12:50360927-50360941 chr12:50360919-50360932 chr12:50360926-50360945

No.	Distal block	Cell Line	Cell type
1	chr12:50358701..50362803-chr12:50449341..50451682,4	MCF-7	breast:
2	chr12:50359856..50363195-chr12:50464299..50467277,4	MCF-7	breast:
3	chr12:50362033..50363685-chr12:50379610..50381169,2	K562	blood:
4	chr12:50361163..50363530-chr12:50480860..50483276,2	MCF-7	breast:
5	chr12:50361058..50363357-chr12:50474948..50477401,2	MCF-7	breast:
6	chr12:50362211..50363749-chr12:50366597..50368397,2	K562	blood:
7	chr12:50361097..50363136-chr12:50368065..50369960,2	MCF-7	breast:
8	chr12:50348137..50350764-chr12:50360835..50363285,2	K562	blood:

Variant related genes	Relation type
AQP6	TF binding region
ENSG00000086159	Chromatin interaction
ENSG00000257378	Chromatin interaction
ENSG00000110881	Chromatin interaction
ENSG00000066117	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12306363	0.89[EUR][1000 genomes]
rs17124205	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17124219	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17124220	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3741560	0.91[AMR][1000 genomes];0.89[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:36 , 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	chr12:50361600-50362600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:50361600-50362600	Flanking Bivalent TSS/Enh	HepG2	liver
6	chr12:50361600-50362800	Weak transcription	HSMM	muscle
7	chr12:50361600-50363000	Enhancers	Liver	Liver
8	chr12:50361600-50364400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr12:50361600-50368200	Weak transcription	Right Atrium	heart
10	chr12:50361800-50362400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
11	chr12:50361800-50362400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:50361800-50362400	Enhancers	Brain Germinal Matrix	brain
13	chr12:50361800-50362800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:50361800-50363000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:50361800-50363800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
16	chr12:50361800-50364000	Enhancers	Brain Angular Gyrus	brain
17	chr12:50361800-50364200	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr12:50361800-50364200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:50361800-50364200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:50361800-50364200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:50361800-50364600	Weak transcription	A549	lung
22	chr12:50361800-50364600	Weak transcription	HMEC	breast
23	chr12:50361800-50364800	Enhancers	Brain Cingulate Gyrus	brain
24	chr12:50361800-50365200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:50361800-50365800	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr12:50361800-50366200	Enhancers	Brain Substantia Nigra	brain
27	chr12:50361800-50367800	Enhancers	Brain Hippocampus Middle	brain
28	chr12:50362000-50362400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:50362000-50363800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:50362000-50364000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:50362000-50364400	Weak transcription	NHEK	skin
32	chr12:50362000-50367000	Enhancers	Brain Anterior Caudate	brain
33	chr12:50362000-50371200	Weak transcription	Fetal Brain Female	brain
34	chr12:50362200-50362600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr12:50362200-50362600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:50362200-50363200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links