Variant report

Variant	rs2686842
Chromosome Location	chr7:48015688-48015689
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:48014982..48017328-chr7:48026575..48029341,3	K562	blood:
2	chr7:48013726..48016111-chr7:48043211..48046121,2	K562	blood:
3	chr7:48008512..48011400-chr7:48014003..48016517,2	MCF-7	breast:
4	chr7:48012956..48017232-chr7:48017620..48020627,4	MCF-7	breast:
5	chr7:48003871..48006559-chr7:48013997..48016570,2	K562	blood:

Variant related genes	Relation type
ENSG00000164744	Chromatin interaction
ENSG00000136273	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1056663	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12702401	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13309127	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1879833	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1879834	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2037483	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2037485	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242477	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686830	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2686831	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2686832	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2686833	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2686834	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2686835	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686836	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686838	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2686839	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686840	0.83[AMR][1000 genomes]
rs2686841	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708853	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2708858	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708859	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708861	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708862	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708865	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2708873	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2708877	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708882	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708894	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708895	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708896	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2708897	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708898	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2708902	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708903	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708905	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2952720	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3176478	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3176564	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34016848	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35151200	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35536957	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57995674	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs953572	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs953594	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	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	nsv830991	chr7:47854530-48025996	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2686842	UPP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47999600-48017600	Strong transcription	Primary T cells from cord blood	blood
2	chr7:47999600-48018000	Strong transcription	Fetal Thymus	thymus
3	chr7:48000200-48016600	Strong transcription	Liver	Liver
4	chr7:48000200-48017800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr7:48000400-48016800	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr7:48000400-48017600	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr7:48000400-48017600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr7:48000400-48017600	Strong transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:48000400-48017800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr7:48000400-48017800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr7:48000600-48015800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr7:48000600-48017600	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr7:48001600-48017600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:48002000-48018200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr7:48007400-48018200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr7:48008600-48016200	Weak transcription	Psoas Muscle	Psoas
17	chr7:48009200-48016800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr7:48009600-48018000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr7:48009800-48018000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr7:48010000-48018000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr7:48010200-48017600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr7:48010200-48017800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr7:48010200-48017800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr7:48010200-48018200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr7:48010400-48017600	Strong transcription	Stomach Smooth Muscle	stomach
26	chr7:48010400-48018000	Strong transcription	Fetal Muscle Leg	muscle
27	chr7:48010400-48018200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr7:48010600-48017800	Strong transcription	Brain Anterior Caudate	brain
29	chr7:48010600-48018000	Strong transcription	Primary B cells from cord blood	blood
30	chr7:48010600-48018000	Strong transcription	Fetal Lung	lung
31	chr7:48010800-48016800	Strong transcription	Adipose Nuclei	Adipose
32	chr7:48010800-48017200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr7:48010800-48017600	Strong transcription	Hela-S3	cervix
34	chr7:48010800-48018000	Strong transcription	Fetal Muscle Trunk	muscle
35	chr7:48010800-48018000	Strong transcription	Placenta	Placenta
36	chr7:48010800-48018000	Strong transcription	Fetal Stomach	stomach
37	chr7:48010800-48018000	Strong transcription	Spleen	Spleen
38	chr7:48011000-48016200	Strong transcription	Aorta	Aorta
39	chr7:48011000-48017200	Strong transcription	Brain Germinal Matrix	brain
40	chr7:48011000-48017400	Strong transcription	Lung	lung
41	chr7:48011000-48017600	Strong transcription	HSMMtube	muscle
42	chr7:48011000-48017800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr7:48011000-48017800	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr7:48011000-48018000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr7:48011000-48018200	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr7:48011200-48017200	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr7:48011200-48017600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr7:48011200-48017800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:48011200-48017800	Strong transcription	Brain Angular Gyrus	brain
50	chr7:48011200-48017800	Strong transcription	NH-A	brain

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