Variant report

Variant	rs13228657
Chromosome Location	chr7:48179177-48179178
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:48179050..48179761-chr7:48194036..48194625,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10215134	0.83[ASN][1000 genomes]
rs10224302	0.83[ASN][1000 genomes]
rs10224538	0.83[ASN][1000 genomes]
rs10227666	0.83[ASN][1000 genomes]
rs10227773	0.83[ASN][1000 genomes]
rs10227781	0.83[ASN][1000 genomes]
rs10253481	0.83[ASN][1000 genomes]
rs10257019	0.83[ASN][1000 genomes]
rs10282492	0.80[ASN][1000 genomes]
rs10951949	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10951950	0.83[ASN][1000 genomes]
rs11972396	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12540937	0.83[ASN][1000 genomes]
rs35739625	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6415281	0.90[ASN][1000 genomes]
rs6463466	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6463468	0.91[ASN][1000 genomes]
rs6463469	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6463471	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6945143	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6949697	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6950146	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6950379	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6950479	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6962799	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6968320	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6968324	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6968353	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6968461	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6968474	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6969934	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6970283	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6971078	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6972786	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6972898	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6975386	0.84[EUR][1000 genomes]
rs6975408	0.84[EUR][1000 genomes]
rs7455086	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7455481	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7457043	0.83[ASN][1000 genomes]
rs7457060	0.83[ASN][1000 genomes]
rs7802128	0.83[ASN][1000 genomes]
rs9639995	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9639996	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
3	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1027414	chr7:48117684-48438543	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1033738	chr7:48143988-48349357	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13228657	UPP1	cis	Artery Tibial	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48171000-48179800	Weak transcription	NH-A	brain
2	chr7:48174400-48186600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:48175200-48179800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr7:48177800-48179200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr7:48178400-48179400	Enhancers	Liver	Liver
6	chr7:48178400-48179800	Flanking Active TSS	HepG2	liver
7	chr7:48178400-48181000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr7:48178600-48179400	Enhancers	A549	lung
9	chr7:48178600-48179600	Enhancers	Duodenum Mucosa	Duodenum
10	chr7:48178600-48180600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr7:48178600-48181400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr7:48178800-48179800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr7:48178800-48180000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr7:48178800-48180000	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr7:48178800-48181200	Enhancers	Small Intestine	intestine
16	chr7:48179000-48179800	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr7:48179000-48180400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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