Variant report

Variant	rs2272571
Chromosome Location	chr17:18047189-18047190
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17991175..17992714-chr17:18046165..18048704,2	K562	blood:
2	chr17:18045055..18047545-chr17:18085965..18089684,5	K562	blood:
3	chr17:18046909..18048719-chr17:18053512..18055928,2	K562	blood:
4	chr17:18007764..18010490-chr17:18045760..18048651,2	MCF-7	breast:
5	chr17:18044857..18048212-chr17:18048916..18052109,4	MCF-7	breast:
6	chr17:18044679..18047861-chr17:18085770..18088322,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091536	Chromatin interaction
ENSG00000091542	Chromatin interaction
ENSG00000108591	Chromatin interaction
ENSG00000266677	Chromatin interaction
ENSG00000238691	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1064629	0.83[EUR][1000 genomes]
rs12449609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12450483	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2056841	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072652	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072653	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2075659	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242595	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4925145	0.82[CHD][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4925147	0.83[EUR][1000 genomes]
rs57186648	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58804619	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59179192	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72827432	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8068517	0.86[CEU][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv907769	chr17:18000321-18064195	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv907770	chr17:18003845-18098018	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv907771	chr17:18013560-18098018	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv470580	chr17:18029857-18060192	Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
11	nsv907772	chr17:18030524-18098018	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv510702	chr17:18037676-18116801	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2272571	SNORD49B	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18040600-18056000	Weak transcription	Gastric	stomach
2	chr17:18040800-18056400	Weak transcription	Right Atrium	heart
3	chr17:18044600-18052200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:18044600-18053600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr17:18044800-18047200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
6	chr17:18045000-18056600	Weak transcription	Fetal Intestine Small	intestine
7	chr17:18045200-18056600	Weak transcription	Esophagus	oesophagus
8	chr17:18046000-18047400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr17:18046000-18047400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr17:18046200-18047200	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr17:18046200-18047400	Enhancers	H1 Cell Line	embryonic stem cell
12	chr17:18046200-18047400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr17:18046200-18047400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr17:18046200-18047400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr17:18046600-18047200	Enhancers	Lung	lung
16	chr17:18046600-18056000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr17:18046800-18047400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr17:18046800-18047800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr17:18046800-18048000	Enhancers	Fetal Muscle Trunk	muscle
20	chr17:18047000-18047200	Bivalent/Poised TSS	HepG2	liver
21	chr17:18047000-18047600	Bivalent Enhancer	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links