Variant report

Variant	rs2708902
Chromosome Location	chr7:48003364-48003365
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1056663	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12702401	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13309127	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1879833	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1879834	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2037483	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2037485	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242477	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2242478	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2242479	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2686820	0.82[EUR][1000 genomes]
rs2686821	0.82[EUR][1000 genomes]
rs2686823	0.82[EUR][1000 genomes]
rs2686825	0.82[EUR][1000 genomes]
rs2686830	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686831	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686832	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686833	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686834	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686835	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2686836	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2686838	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686839	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2686840	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2686841	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686842	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708853	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2708858	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708859	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708861	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708862	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708865	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2708873	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2708875	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2708877	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708878	0.82[EUR][1000 genomes]
rs2708880	0.82[EUR][1000 genomes]
rs2708881	0.82[EUR][1000 genomes]
rs2708882	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708894	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708895	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708896	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2708897	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708898	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708903	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708905	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2708910	0.82[EUR][1000 genomes]
rs2708911	0.82[EUR][1000 genomes]
rs2952720	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3176478	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3176564	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34016848	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35151200	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35536957	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57995674	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60107343	0.82[EUR][1000 genomes]
rs885337	0.82[EUR][1000 genomes]
rs939904	0.82[EUR][1000 genomes]
rs939905	0.82[EUR][1000 genomes]
rs953572	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs953594	0.81[AMR][1000 genomes];0.85[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2708902	PKD1L1	cis	cerebellar cortex	BrainEAC
rs2708902	PKD1L1	cis	brain	BrainEAC
rs2708902	UPP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47986400-48003800	Weak transcription	Fetal Brain Male	brain
2	chr7:47991400-48003600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:47991400-48004800	Weak transcription	Fetal Kidney	kidney
4	chr7:47992000-48004400	Weak transcription	Stomach Mucosa	stomach
5	chr7:47992200-48005200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:47995800-48004000	Weak transcription	K562	blood
7	chr7:47999400-48005000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr7:47999400-48008800	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr7:47999600-48017600	Strong transcription	Primary T cells from cord blood	blood
10	chr7:47999600-48018000	Strong transcription	Fetal Thymus	thymus
11	chr7:48000200-48008400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:48000200-48008600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:48000200-48008600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr7:48000200-48008800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr7:48000200-48008800	Strong transcription	HSMM	muscle
16	chr7:48000200-48009400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:48000200-48009400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr7:48000200-48016600	Strong transcription	Liver	Liver
19	chr7:48000200-48017800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:48000400-48004800	Strong transcription	Brain Hippocampus Middle	brain
21	chr7:48000400-48005200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr7:48000400-48007200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
23	chr7:48000400-48007400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr7:48000400-48007800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr7:48000400-48007800	Strong transcription	Fetal Brain Female	brain
26	chr7:48000400-48008200	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr7:48000400-48008400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr7:48000400-48008400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr7:48000400-48008400	Strong transcription	Adipose Nuclei	Adipose
30	chr7:48000400-48008400	Strong transcription	Fetal Lung	lung
31	chr7:48000400-48008600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr7:48000400-48008600	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr7:48000400-48008600	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr7:48000400-48008600	Strong transcription	Stomach Smooth Muscle	stomach
35	chr7:48000400-48008600	Strong transcription	NH-A	brain
36	chr7:48000400-48008800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr7:48000400-48008800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr7:48000400-48009000	Strong transcription	Primary B cells from peripheral blood	blood
39	chr7:48000400-48009000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr7:48000400-48009000	Strong transcription	Fetal Intestine Large	intestine
41	chr7:48000400-48009400	Strong transcription	Osteobl	bone
42	chr7:48000400-48009600	Strong transcription	A549	lung
43	chr7:48000400-48010000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr7:48000400-48011200	Strong transcription	Colon Smooth Muscle	Colon
45	chr7:48000400-48016800	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr7:48000400-48017600	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr7:48000400-48017600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr7:48000400-48017600	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr7:48000400-48017800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr7:48000400-48017800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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