Variant report

Variant	rs297920
Chromosome Location	chr12:50280536-50280537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50279366..50281726-chr12:50476723..50478563,2	MCF-7	breast:
2	chr12:50275093..50276632-chr12:50278592..50280741,2	K562	blood:
3	chr12:50270045..50272990-chr12:50279975..50282889,2	MCF-7	breast:
4	chr12:50278683..50281665-chr12:50304912..50306489,2	MCF-7	breast:
5	chr12:50280227..50282176-chr12:50287942..50290577,2	K562	blood:
6	chr12:50272122..50274588-chr12:50280399..50282303,2	MCF-7	breast:
7	chr12:50273812..50276593-chr12:50279241..50281059,2	K562	blood:
8	chr12:50275514..50280639-chr12:50281373..50284133,6	MCF-7	breast:
9	chr12:50278311..50281286-chr12:50298604..50300536,3	MCF-7	breast:
10	chr12:50280144..50282226-chr12:50283386..50285640,2	K562	blood:
11	chr12:50172716..50175610-chr12:50278346..50281204,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257771	Chromatin interaction
ENSG00000258135	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs297919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs297921	1.00[AFR][1000 genomes]
rs297925	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs297926	1.00[AMR][1000 genomes]
rs297927	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs297928	0.88[AFR][1000 genomes]
rs297929	1.00[AMR][1000 genomes]
rs297930	0.88[AFR][1000 genomes]
rs584830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs585255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs695061	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50267000-50297000	Weak transcription	Right Atrium	heart
2	chr12:50275000-50294800	Weak transcription	Fetal Brain Male	brain
3	chr12:50275200-50282000	Weak transcription	Gastric	stomach
4	chr12:50277800-50288000	Strong transcription	Brain Hippocampus Middle	brain
5	chr12:50278800-50286200	Strong transcription	Brain Inferior Temporal Lobe	brain
6	chr12:50278800-50286200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:50279000-50285000	Strong transcription	Brain Germinal Matrix	brain
8	chr12:50279000-50286000	Strong transcription	Brain Anterior Caudate	brain
9	chr12:50279200-50288000	Strong transcription	Brain Cingulate Gyrus	brain
10	chr12:50279400-50281400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:50279400-50281800	Strong transcription	Brain Substantia Nigra	brain
12	chr12:50279400-50281800	Weak transcription	Hela-S3	cervix
13	chr12:50279400-50286600	Strong transcription	Brain Angular Gyrus	brain
14	chr12:50279600-50281200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:50279600-50281800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:50279600-50281800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:50279600-50285400	Strong transcription	Fetal Brain Female	brain
18	chr12:50279800-50280800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:50279800-50280800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr12:50279800-50280800	Weak transcription	Fetal Muscle Leg	muscle
21	chr12:50279800-50281000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr12:50279800-50281000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:50279800-50281000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr12:50279800-50281000	Enhancers	HepG2	liver
25	chr12:50279800-50281200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:50280000-50282800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:50280200-50280600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:50280200-50281000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:50280200-50282000	Weak transcription	Pancreas	Pancrea

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