Variant report

Variant	rs72799275
Chromosome Location	chr2:54179050-54179051
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:54178745-54179071	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54174802..54180100-chr2:54196834..54199105,5	K562	blood:
2	chr2:54166145..54169657-chr2:54176630..54180316,3	K562	blood:
3	chr2:54176939..54180611-chr2:54194148..54196574,3	K562	blood:
4	chr2:54178658..54180382-chr2:54186719..54189310,2	K562	blood:
5	chr2:54177874..54180266-chr2:54264594..54267225,2	K562	blood:
6	chr2:54173684..54175896-chr2:54177409..54179300,2	K562	blood:
7	chr2:54166205..54169657-chr2:54178051..54180434,3	K562	blood:

No data

Variant related genes	Relation type
PSME4	TF binding region
ENSG00000068878	Chromatin interaction
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10204047	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10204432	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10490472	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10490473	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13387421	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13404007	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13426962	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17039534	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17045239	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17045241	0.93[EUR][1000 genomes]
rs17045262	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17045286	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17045296	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2056650	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2287339	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2287342	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2287346	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2302876	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2302880	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28834518	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3213774	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3755113	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3755114	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3755115	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3755116	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3770390	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3770391	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3815650	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3821079	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6761242	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72799242	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72799293	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72901302	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72902916	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72902923	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72902926	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72902929	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72902937	0.81[AMR][1000 genomes]
rs7601553	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605552	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][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	nsv829423	chr2:54177847-54181052	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54087600-54187600	Weak transcription	Stomach Mucosa	stomach
2	chr2:54109800-54179800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:54151000-54189800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:54153200-54179800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:54153400-54194600	Weak transcription	Fetal Brain Male	brain
6	chr2:54156600-54188000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:54156600-54190000	Weak transcription	Spleen	Spleen
8	chr2:54159200-54188000	Weak transcription	Colonic Mucosa	Colon
9	chr2:54159200-54188000	Weak transcription	Esophagus	oesophagus
10	chr2:54159200-54188200	Weak transcription	Small Intestine	intestine
11	chr2:54159200-54189400	Weak transcription	Aorta	Aorta
12	chr2:54159200-54189800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:54159400-54195800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:54160800-54179400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:54161600-54189800	Weak transcription	Ovary	ovary
16	chr2:54163600-54180400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:54171000-54188600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:54172800-54179200	Weak transcription	Brain Angular Gyrus	brain
19	chr2:54172800-54184400	Weak transcription	Brain Anterior Caudate	brain
20	chr2:54172800-54184600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:54173400-54191400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr2:54174000-54184600	Weak transcription	Left Ventricle	heart
23	chr2:54174200-54195600	Weak transcription	Thymus	Thymus
24	chr2:54174400-54179600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:54174400-54180000	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr2:54174400-54182800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:54174400-54184200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr2:54174400-54184600	Weak transcription	Colon Smooth Muscle	Colon
29	chr2:54174400-54188000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:54174400-54188600	Weak transcription	GM12878-XiMat	blood
31	chr2:54174600-54180400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:54175000-54179800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:54175200-54179200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:54175200-54193000	Weak transcription	Fetal Intestine Small	intestine
35	chr2:54175200-54195400	Weak transcription	Fetal Stomach	stomach
36	chr2:54175400-54188400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:54175600-54184200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr2:54175800-54184400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:54175800-54189800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr2:54175800-54190000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:54176000-54179800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:54176000-54184600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr2:54176000-54187800	Weak transcription	Fetal Muscle Leg	muscle
44	chr2:54176000-54189800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:54176200-54179400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:54176200-54180000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:54176200-54180200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:54176200-54182800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:54176200-54184000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr2:54176200-54184600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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