Variant report

Variant	rs1004808
Chromosome Location	chr3:53140630-53140631
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53139091..53142034-chr3:53144665..53147558,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1004807	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2253675	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2336724	0.86[AMR][1000 genomes]
rs2564922	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2564929	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2564939	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2581798	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55950520	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56058643	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56386026	0.82[EUR][1000 genomes]
rs60579898	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62255925	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62255929	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62255931	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73082047	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs930122	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv590356	chr3:53134098-53170500	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1004808	SERBP1P3	cis	lung	GTEx
rs1004808	SERBP1P3	cis	Thyroid	GTEx
rs1004808	RFT1	cis	Artery Aorta	GTEx
rs1004808	RFT1	cis	Artery Tibial	GTEx
rs1004808	RFT1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53107800-53151400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:53117800-53147200	Weak transcription	Psoas Muscle	Psoas
3	chr3:53119000-53154200	Weak transcription	Stomach Mucosa	stomach
4	chr3:53120800-53144400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:53121400-53142600	Strong transcription	Stomach Smooth Muscle	stomach
6	chr3:53122400-53143200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:53122800-53152200	Weak transcription	Small Intestine	intestine
8	chr3:53123200-53148600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr3:53124200-53151600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:53127000-53154200	Weak transcription	Right Atrium	heart
11	chr3:53127400-53144000	Weak transcription	Fetal Heart	heart
12	chr3:53130800-53146400	Strong transcription	Fetal Intestine Large	intestine
13	chr3:53131600-53140800	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:53131600-53144000	Strong transcription	Liver	Liver
15	chr3:53131800-53140800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:53132000-53141800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:53132000-53148000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr3:53133600-53152600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:53133800-53144000	Weak transcription	Fetal Kidney	kidney
20	chr3:53134800-53143600	Strong transcription	Placenta	Placenta
21	chr3:53135000-53140800	Strong transcription	Brain Hippocampus Middle	brain
22	chr3:53135000-53144600	Strong transcription	Lung	lung
23	chr3:53135200-53141400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:53135200-53143000	Strong transcription	Fetal Stomach	stomach
25	chr3:53135200-53146000	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:53135400-53140800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr3:53135400-53141000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:53135600-53143200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:53135600-53146200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:53136000-53140800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:53136600-53145600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:53136800-53143400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr3:53137200-53143800	Weak transcription	A549	lung
34	chr3:53137200-53146200	Strong transcription	Duodenum Mucosa	Duodenum
35	chr3:53137400-53141200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:53137400-53143000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:53137400-53143600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:53137400-53144000	Weak transcription	K562	blood
39	chr3:53137400-53151400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:53137400-53161600	Strong transcription	Fetal Intestine Small	intestine
41	chr3:53137600-53147800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr3:53137800-53143000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:53138000-53151000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:53138200-53141800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr3:53138200-53143000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:53138200-53143200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:53138200-53143200	Strong transcription	Fetal Muscle Leg	muscle
48	chr3:53138200-53143800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr3:53138400-53141800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr3:53138400-53141800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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