Variant report

Variant	rs393744
Chromosome Location	chr20:52578414-52578415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:732113..733855-chr20:52577889..52580528,2	MCF-7	breast:
2	chr17:55980748..55982351-chr20:52577090..52579226,2	MCF-7	breast:
3	chr20:52572078..52574056-chr20:52577646..52580045,2	K562	blood:
4	chr20:52576980..52579771-chr20:52581907..52583862,2	K562	blood:
5	chr20:52577489..52580206-chr6:39156376..39158164,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161999	Chromatin interaction
ENSG00000180891	Chromatin interaction
ENSG00000103266	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs119069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs119071	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs208360	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs208368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs208371	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs208380	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2158977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs375769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs390573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6013869	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
3	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
4	nsv1055549	chr20:52555871-52586281	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52567000-52580200	Weak transcription	Stomach Mucosa	stomach
3	chr20:52570200-52591800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr20:52570200-52592400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr20:52570800-52590800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr20:52576400-52578600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr20:52576400-52578600	Enhancers	Brain Hippocampus Middle	brain
8	chr20:52576400-52591400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr20:52576600-52578600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr20:52576600-52578600	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr20:52576800-52579200	Enhancers	NHDF-Ad	bronchial
12	chr20:52577000-52580400	Weak transcription	Fetal Muscle Leg	muscle
13	chr20:52577200-52578600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr20:52577200-52578800	Bivalent Enhancer	HUVEC	blood vessel
15	chr20:52577400-52578800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr20:52578000-52578600	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr20:52578000-52578600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr20:52578000-52578600	Enhancers	Primary T cells from cord blood	blood
19	chr20:52578200-52578600	Enhancers	H9 Cell Line	embryonic stem cell
20	chr20:52578200-52578600	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr20:52578200-52578600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr20:52578200-52578600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr20:52578200-52578600	Enhancers	Brain Angular Gyrus	brain
24	chr20:52578200-52578600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr20:52578200-52578800	Enhancers	H1 Cell Line	embryonic stem cell
26	chr20:52578200-52578800	Enhancers	Brain Anterior Caudate	brain
27	chr20:52578200-52578800	Enhancers	Brain Substantia Nigra	brain
28	chr20:52578400-52578600	Active TSS	Fetal Kidney	kidney
29	chr20:52578400-52578600	Bivalent Enhancer	Small Intestine	intestine
30	chr20:52578400-52580200	Weak transcription	Fetal Stomach	stomach
31	chr20:52578400-52591200	Weak transcription	HSMMtube	muscle

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