Variant report

Variant	rs59862432
Chromosome Location	chr12:50301121-50301122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50293107..50297008-chr12:50298407..50301335,3	MCF-7	breast:
2	chr12:50283500..50287015-chr12:50298892..50302094,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135472	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12306966	0.94[AFR][1000 genomes]
rs12312614	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12422556	0.83[ASN][1000 genomes]
rs12422575	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12424035	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12424268	0.84[ASN][1000 genomes]
rs12424404	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12426614	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12426750	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12427024	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12427051	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17124131	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs184172	0.91[ASN][1000 genomes]
rs2276187	0.91[EUR][1000 genomes]
rs2298640	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298641	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55984325	0.91[EUR][1000 genomes]
rs58494052	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61416142	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72644872	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72644873	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72644874	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72644875	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72644876	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv525920	chr12:50285061-50304949	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv558836	chr12:50290023-50316439	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50295200-50303000	Weak transcription	K562	blood
2	chr12:50298200-50303000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:50298200-50307800	Weak transcription	Right Atrium	heart
4	chr12:50298400-50301200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:50298400-50303200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:50298400-50308000	Weak transcription	Pancreas	Pancrea
7	chr12:50298600-50301200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:50298600-50303000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:50298600-50303400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr12:50299000-50301200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr12:50299600-50303400	Weak transcription	Brain Germinal Matrix	brain
12	chr12:50300200-50301400	Enhancers	Hela-S3	cervix
13	chr12:50300200-50301600	Enhancers	Brain Anterior Caudate	brain
14	chr12:50300400-50301600	Enhancers	Brain Hippocampus Middle	brain
15	chr12:50300800-50301600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:50301000-50301200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:50301000-50301200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:50301000-50301400	Enhancers	HSMM	muscle
19	chr12:50301000-50301600	Enhancers	Brain Angular Gyrus	brain
20	chr12:50301000-50301600	Enhancers	HSMMtube	muscle
21	chr12:50301000-50301800	Enhancers	Brain Substantia Nigra	brain
22	chr12:50301000-50302000	Enhancers	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links