Variant report

Variant	rs7800590
Chromosome Location	chr7:48041945-48041946
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	chr7:48016950..48019113-chr7:48039129..48042039,2	K562	blood:

Variant related genes	Relation type
ENSG00000136273	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10253220	0.86[AMR][1000 genomes]
rs10253238	0.86[ASN][1000 genomes]
rs10261930	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10951937	0.83[ASN][1000 genomes]
rs10951938	0.83[ASN][1000 genomes]
rs10951940	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10951941	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10951942	0.82[AMR][1000 genomes]
rs11766144	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11766891	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11767002	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11772387	0.87[AMR][1000 genomes]
rs11773348	0.83[ASN][1000 genomes]
rs12535580	0.86[AMR][1000 genomes]
rs12702405	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12702406	0.87[AMR][1000 genomes]
rs13230023	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1574242	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1915960	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1915962	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1915966	0.86[AMR][1000 genomes]
rs1915967	0.80[AMR][1000 genomes]
rs1915971	0.80[AMR][1000 genomes]
rs1915972	0.83[AMR][1000 genomes]
rs2348670	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2881991	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2881992	0.86[ASN][1000 genomes]
rs4332046	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4618593	0.83[ASN][1000 genomes]
rs6979699	0.81[AMR][1000 genomes]
rs7357251	0.82[AMR][1000 genomes]
rs7779252	0.80[AMR][1000 genomes]
rs7791084	0.86[ASN][1000 genomes]
rs7791572	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7791823	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7807611	0.86[ASN][1000 genomes]
rs7807612	0.86[ASN][1000 genomes]
rs7807654	0.86[ASN][1000 genomes]
rs7807750	0.86[ASN][1000 genomes]
rs7808462	0.86[ASN][1000 genomes]
rs9690905	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	nsv888004	chr7:48028771-48120717	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3399205	chr7:48041575-48042174	Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3477206	chr7:48041579-48042160	Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv3520765	chr7:48041582-48042133	Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv3520766	chr7:48041582-48042133	Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv3378762	chr7:48041633-48042137	Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv3477205	chr7:48041671-48042126	Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv3408982	chr7:48041674-48042104	Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv3477207	chr7:48041733-48042072	Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7800590	UPP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48031800-48043600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:48031800-48050200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:48039000-48044000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:48040000-48046600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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