Variant report

Variant	rs2708891
Chromosome Location	chr7:48032595-48032596
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:48016045..48020914-chr7:48030569..48033658,6	K562	blood:
2	chr7:48031095..48033453-chr7:48087493..48089900,2	K562	blood:
3	chr7:48017886..48020914-chr7:48029520..48034474,4	K562	blood:
4	chr7:48032161..48032696-chr7:48149524..48150293,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136273	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2686783	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2708851	0.84[EUR][1000 genomes]
rs2708883	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2708884	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2708885	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708901	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708909	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6944437	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6962900	0.86[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2708891	UPP1	Cis_1M	lymphoblastoid	RTeQTL
rs2708891	UPP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48031800-48032600	Flanking Active TSS	Primary T cells from cord blood	blood
2	chr7:48031800-48032800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr7:48031800-48032800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr7:48031800-48039200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:48031800-48039800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr7:48031800-48039800	Weak transcription	Esophagus	oesophagus
7	chr7:48031800-48043600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:48031800-48050200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:48032000-48032600	Enhancers	Primary T cells fromperipheralblood	blood
10	chr7:48032000-48032600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:48032000-48032600	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr7:48032000-48032600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr7:48032000-48032600	Enhancers	Fetal Intestine Large	intestine
14	chr7:48032000-48032600	Enhancers	Fetal Intestine Small	intestine
15	chr7:48032000-48032800	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr7:48032000-48032800	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr7:48032000-48032800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr7:48032000-48032800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr7:48032000-48032800	Enhancers	Fetal Thymus	thymus
20	chr7:48032000-48033000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr7:48032000-48034400	Weak transcription	Pancreas	Pancrea
22	chr7:48032200-48032600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr7:48032200-48032600	Enhancers	Primary hematopoietic stem cells	blood
24	chr7:48032200-48032600	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr7:48032200-48032600	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr7:48032200-48032600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:48032200-48032600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr7:48032200-48032800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr7:48032200-48032800	Enhancers	Stomach Mucosa	stomach
30	chr7:48032200-48033000	Enhancers	Primary T killer memory cells from peripheral blood	blood

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