Variant report

Variant	rs805340
Chromosome Location	chr2:54189069-54189070
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54178658..54180382-chr2:54186719..54189310,2	K562	blood:
2	chr2:54188266..54193064-chr2:54193123..54200059,18	K562	blood:
3	chr2:54182457..54184088-chr2:54186871..54190215,3	K562	blood:

Variant related genes	Relation type
ENSG00000068878	Chromatin interaction
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1232	0.86[AMR][1000 genomes]
rs2909459	0.85[AMR][1000 genomes]
rs2949810	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2949814	0.91[AMR][1000 genomes]
rs4671746	0.82[AMR][1000 genomes]
rs55692047	0.82[AMR][1000 genomes]
rs56302494	0.82[AMR][1000 genomes]
rs62139336	0.83[AMR][1000 genomes]
rs805311	0.91[AMR][1000 genomes]
rs805313	0.81[AMR][1000 genomes]
rs805316	0.92[AMR][1000 genomes]
rs805325	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs805326	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs805327	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs805334	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs805337	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs805338	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs805351	0.82[AMR][1000 genomes]
rs805352	0.82[AMR][1000 genomes]
rs805354	0.82[AMR][1000 genomes]
rs805355	0.82[AMR][1000 genomes]
rs805356	0.82[AMR][1000 genomes]
rs805357	0.82[AMR][1000 genomes]
rs805362	0.82[AMR][1000 genomes]
rs805368	0.88[AMR][1000 genomes]
rs805383	0.89[AMR][1000 genomes]
rs805385	0.92[AMR][1000 genomes]
rs805397	0.81[AMR][1000 genomes]
rs805398	0.94[AMR][1000 genomes]
rs805401	0.81[AMR][1000 genomes]
rs805404	0.81[AMR][1000 genomes]
rs805413	0.94[AMR][1000 genomes]
rs805446	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs805447	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs805449	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs805451	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs809281	0.97[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	esv2762257	chr2:54187617-54192015	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs805340	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54151000-54189800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:54153400-54194600	Weak transcription	Fetal Brain Male	brain
3	chr2:54156600-54190000	Weak transcription	Spleen	Spleen
4	chr2:54159200-54189400	Weak transcription	Aorta	Aorta
5	chr2:54159200-54189800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:54159400-54195800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:54161600-54189800	Weak transcription	Ovary	ovary
8	chr2:54173400-54191400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:54174200-54195600	Weak transcription	Thymus	Thymus
10	chr2:54175200-54193000	Weak transcription	Fetal Intestine Small	intestine
11	chr2:54175200-54195400	Weak transcription	Fetal Stomach	stomach
12	chr2:54175800-54189800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:54175800-54190000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:54176000-54189800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:54176200-54189800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:54176200-54189800	Weak transcription	NH-A	brain
17	chr2:54176200-54191600	Weak transcription	NHDF-Ad	bronchial
18	chr2:54176200-54192000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:54176200-54194200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:54176200-54194600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:54176200-54195400	Weak transcription	Fetal Intestine Large	intestine
22	chr2:54176200-54195400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr2:54176200-54196000	Weak transcription	Fetal Thymus	thymus
24	chr2:54176200-54196200	Weak transcription	Placenta	Placenta
25	chr2:54176400-54194800	Weak transcription	NHLF	lung
26	chr2:54176400-54195000	Weak transcription	HSMM	muscle
27	chr2:54176600-54189200	Weak transcription	Adipose Nuclei	Adipose
28	chr2:54176800-54192200	Weak transcription	Hela-S3	cervix
29	chr2:54177000-54189800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:54177000-54189800	Weak transcription	Dnd41	blood
31	chr2:54177000-54194800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:54177400-54189600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr2:54177400-54189800	Weak transcription	Lung	lung
34	chr2:54177400-54190000	Weak transcription	Gastric	stomach
35	chr2:54177400-54191000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:54177400-54194400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:54177600-54189200	Weak transcription	HepG2	liver
38	chr2:54177800-54195400	Weak transcription	Right Ventricle	heart
39	chr2:54179400-54189800	Weak transcription	Psoas Muscle	Psoas
40	chr2:54180000-54189800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:54180000-54195400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:54180400-54189600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr2:54180400-54191800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr2:54183200-54190400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:54184800-54189600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:54184800-54190200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr2:54185000-54189400	Weak transcription	Fetal Heart	heart
48	chr2:54185000-54189800	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:54185200-54189400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr2:54185800-54189600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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