Variant report

Variant	rs402992
Chromosome Location	chr20:52577607-52577608
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:55980748..55982351-chr20:52577090..52579226,2	MCF-7	breast:
2	chr1:201118101..201120636-chr20:52576111..52577980,2	MCF-7	breast:
3	chr12:120729283..120731029-chr20:52576003..52578392,2	MCF-7	breast:
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
ENSG00000202538	Chromatin interaction
ENSG00000180891	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10485440	0.95[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs2024065	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs2024066	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276510	0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2276514	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs371096	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs382133	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs431061	1.00[CEU][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4809946	0.83[JPT][hapmap]
rs4809947	0.83[JPT][hapmap]
rs6013853	0.80[YRI][hapmap]
rs6022877	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6091793	0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs6091794	0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs6097716	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7272317	1.00[JPT][hapmap]
rs872923	0.94[JPT][hapmap]
rs872924	0.88[JPT][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:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52567000-52578200	Weak transcription	Brain Angular Gyrus	brain
3	chr20:52567000-52580200	Weak transcription	Stomach Mucosa	stomach
4	chr20:52570200-52591800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr20:52570200-52592400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr20:52570800-52590800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr20:52574800-52578200	Weak transcription	Brain Substantia Nigra	brain
8	chr20:52575600-52578400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr20:52576200-52577800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr20:52576400-52577800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr20:52576400-52578200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr20:52576400-52578200	Enhancers	Fetal Kidney	kidney
13	chr20:52576400-52578400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr20:52576400-52578400	Enhancers	HSMM	muscle
15	chr20:52576400-52578600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr20:52576400-52578600	Enhancers	Brain Hippocampus Middle	brain
17	chr20:52576400-52591400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr20:52576600-52578000	Enhancers	A549	lung
19	chr20:52576600-52578600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr20:52576600-52578600	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr20:52576800-52577800	Enhancers	Adipose Nuclei	Adipose
22	chr20:52576800-52578200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr20:52576800-52579200	Enhancers	NHDF-Ad	bronchial
24	chr20:52577000-52577800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr20:52577000-52578000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr20:52577000-52578000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr20:52577000-52578000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr20:52577000-52578200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr20:52577000-52578400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr20:52577000-52580400	Weak transcription	Fetal Muscle Leg	muscle
31	chr20:52577200-52577800	Enhancers	Liver	Liver
32	chr20:52577200-52578000	Weak transcription	HSMMtube	muscle
33	chr20:52577200-52578600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr20:52577200-52578800	Bivalent Enhancer	HUVEC	blood vessel
35	chr20:52577400-52577800	Enhancers	NHLF	lung
36	chr20:52577400-52578000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr20:52577400-52578200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr20:52577400-52578200	Weak transcription	Brain Anterior Caudate	brain
39	chr20:52577400-52578200	Weak transcription	Fetal Stomach	stomach
40	chr20:52577400-52578800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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