Variant report

Variant	rs2686833
Chromosome Location	chr7:47995877-47995878
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PKD1L1-1	chr7:47994962-47996911	NONHSAT120522

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1056663	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12702401	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13309127	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1879833	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037483	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2037485	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242477	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242478	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242479	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686820	0.86[EUR][1000 genomes]
rs2686821	0.86[EUR][1000 genomes]
rs2686823	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2686825	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2686827	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2686830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686831	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686834	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686835	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686836	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686838	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686839	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686840	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2686841	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2686842	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708853	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708858	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708859	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708861	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708862	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708865	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2708873	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2708875	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2708877	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708878	0.86[EUR][1000 genomes]
rs2708880	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2708881	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2708882	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708896	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2708897	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708898	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708902	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708903	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708905	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708910	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2708911	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2952720	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3176478	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3176564	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34016848	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35151200	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35536957	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57995674	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60107343	0.86[EUR][1000 genomes]
rs885337	0.85[EUR][1000 genomes]
rs939904	0.85[EUR][1000 genomes]
rs939905	0.85[EUR][1000 genomes]
rs953572	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs953594	0.84[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
rs2686833	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	chr7:47934000-48001800	Weak transcription	Psoas Muscle	Psoas
2	chr7:47977400-48000600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:47982000-47999400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr7:47983600-48001000	Weak transcription	NHLF	lung
5	chr7:47984800-47996000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:47985000-48001400	Weak transcription	Hela-S3	cervix
7	chr7:47985600-48000600	Weak transcription	Ovary	ovary
8	chr7:47986400-48003800	Weak transcription	Fetal Brain Male	brain
9	chr7:47986800-48001800	Weak transcription	NHEK	skin
10	chr7:47990000-48000600	Weak transcription	Brain Angular Gyrus	brain
11	chr7:47990600-48000600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr7:47991000-48001400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr7:47991400-48001000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr7:47991400-48003600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr7:47991400-48004800	Weak transcription	Fetal Kidney	kidney
16	chr7:47991600-48000600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr7:47991600-48000600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:47992000-48000400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr7:47992000-48000600	Weak transcription	Brain Germinal Matrix	brain
20	chr7:47992000-48001600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr7:47992000-48001600	Weak transcription	Pancreas	Pancrea
22	chr7:47992000-48002400	Weak transcription	HepG2	liver
23	chr7:47992000-48004400	Weak transcription	Stomach Mucosa	stomach
24	chr7:47992200-48005200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr7:47992400-48000200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr7:47992400-48000400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:47992400-48000600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr7:47992600-47996800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr7:47992600-47996800	Strong transcription	Primary B cells from cord blood	blood
30	chr7:47992600-48000400	Weak transcription	Fetal Brain Female	brain
31	chr7:47992800-48000600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr7:47993000-47997000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr7:47993200-47996200	Strong transcription	Fetal Muscle Leg	muscle
34	chr7:47993200-47997200	Strong transcription	Liver	Liver
35	chr7:47993200-47997400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr7:47993200-47998000	Strong transcription	Fetal Muscle Trunk	muscle
37	chr7:47993200-47998400	Strong transcription	Primary T cells from cord blood	blood
38	chr7:47993200-48000600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr7:47993400-47996000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
40	chr7:47993400-47997000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr7:47993600-47996200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr7:47993600-47997000	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr7:47993600-47997400	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr7:47993600-47998200	Strong transcription	Adipose Nuclei	Adipose
45	chr7:47993800-47996000	Strong transcription	Colonic Mucosa	Colon
46	chr7:47993800-47996000	Strong transcription	Thymus	Thymus
47	chr7:47993800-47996200	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr7:47993800-47996400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr7:47993800-47996400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr7:47993800-47996800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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