Variant report

Variant	rs353551
Chromosome Location	chr3:52217088-52217089
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52216306..52219221-chr3:52231951..52233528,2	MCF-7	breast:
2	chr3:52215603..52218284-chr3:52231830..52234673,3	K562	blood:
3	chr3:52216183..52218054-chr3:52225196..52227390,3	K562	blood:

Variant related genes	Relation type
ENSG00000023330	Chromatin interaction
ENSG00000242849	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs104903	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11712164	0.85[CHB][hapmap]
rs164640	0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs181274	0.90[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs187084	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs34656997	0.83[ASN][1000 genomes]
rs352139	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs352140	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs352158	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs352161	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs352162	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs352163	0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs352165	0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs352166	0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs352167	0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs352168	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs352169	0.90[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs352170	0.90[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs352171	0.90[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs411457	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs524986	0.89[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs614288	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
5	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
9	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs353551	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52210000-52218200	Enhancers	Liver	Liver
2	chr3:52212000-52222400	Weak transcription	Stomach Mucosa	stomach
3	chr3:52212800-52219400	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr3:52212800-52223800	Weak transcription	Esophagus	oesophagus
5	chr3:52214600-52221000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr3:52215400-52217400	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr3:52215600-52217200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr3:52215600-52217200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:52215600-52217200	Enhancers	Left Ventricle	heart
10	chr3:52215600-52217400	Enhancers	Spleen	Spleen
11	chr3:52215600-52218800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:52215600-52219600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr3:52215600-52219600	Enhancers	Right Ventricle	heart
14	chr3:52215800-52217200	Enhancers	Right Atrium	heart
15	chr3:52215800-52217400	Enhancers	K562	blood
16	chr3:52215800-52224200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:52216200-52217800	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:52216400-52217200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr3:52216400-52218000	Weak transcription	Adipose Nuclei	Adipose
20	chr3:52216600-52217800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:52216600-52217800	Weak transcription	Placenta	Placenta
22	chr3:52216600-52223600	Enhancers	HepG2	liver
23	chr3:52216800-52217600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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