Variant report

Variant	rs62192761
Chromosome Location	chr2:234392009-234392010
allele	G/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	chr2:234391799-234392061	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:234388753..234400184-chr2:234596527..234603213,35	MCF-7	breast:
2	chr2:234390637..234392583-chr2:234428412..234431131,2	K562	blood:
3	chr2:234386983..234399433-chr2:234613282..234621553,23	MCF-7	breast:
4	chr2:234385374..234387769-chr2:234390767..234392853,2	K562	blood:
5	chr2:234392005..234393999-chr2:234465226..234467759,2	MCF-7	breast:
6	chr2:234386026..234387769-chr2:234390744..234392267,2	K562	blood:
7	chr2:234378675..234382523-chr2:234390792..234394362,4	K562	blood:

No data

Variant related genes	Relation type
USP40	TF binding region
ENSG00000167165	Chromatin interaction
ENSG00000224814	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12472244	0.83[EUR][1000 genomes]
rs62192764	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv1000870	chr2:234333083-234410768	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv3214	chr2:234384436-234416949	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62192761	USP40	Cis_1M	lymphoblastoid	RTeQTL
rs62192761	USP40	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234339600-234394200	Weak transcription	HUVEC	blood vessel
2	chr2:234343000-234393000	Strong transcription	Primary T cells from cord blood	blood
3	chr2:234343000-234402200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:234364000-234411200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:234365800-234393600	Weak transcription	Hela-S3	cervix
6	chr2:234373000-234392200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:234373000-234409800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:234373800-234404400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:234375400-234411200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:234377800-234397200	Weak transcription	Small Intestine	intestine
11	chr2:234378200-234395000	Weak transcription	Right Atrium	heart
12	chr2:234380800-234395000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:234381200-234394800	Strong transcription	Pancreas	Pancrea
14	chr2:234381600-234393400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr2:234381600-234399600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr2:234383000-234395000	Strong transcription	NHLF	lung
17	chr2:234383400-234395400	Strong transcription	Brain Hippocampus Middle	brain
18	chr2:234383400-234400200	Strong transcription	Fetal Intestine Small	intestine
19	chr2:234384000-234392800	Strong transcription	Thymus	Thymus
20	chr2:234384000-234395200	Strong transcription	Liver	Liver
21	chr2:234384000-234412400	Weak transcription	Fetal Heart	heart
22	chr2:234384200-234392800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:234384200-234394400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:234384200-234394400	Strong transcription	Placenta	Placenta
25	chr2:234384200-234394600	Strong transcription	Fetal Thymus	thymus
26	chr2:234384200-234394800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:234384200-234394800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr2:234384200-234395000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:234384400-234395000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:234384400-234395000	Strong transcription	Left Ventricle	heart
31	chr2:234384400-234398200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:234384400-234402200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr2:234384400-234402600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:234384600-234392800	Strong transcription	Right Ventricle	heart
35	chr2:234384600-234395000	Strong transcription	Brain Cingulate Gyrus	brain
36	chr2:234384600-234408400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr2:234384800-234392800	Strong transcription	Spleen	Spleen
38	chr2:234385600-234393800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:234386000-234397600	Weak transcription	Brain Germinal Matrix	brain
40	chr2:234386400-234392600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:234386600-234395000	Strong transcription	HepG2	liver
42	chr2:234386600-234400800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:234386800-234407800	Strong transcription	Fetal Intestine Large	intestine
44	chr2:234387200-234396600	Weak transcription	Psoas Muscle	Psoas
45	chr2:234387400-234394800	Weak transcription	Aorta	Aorta
46	chr2:234387400-234402800	Strong transcription	Adipose Nuclei	Adipose
47	chr2:234387400-234466000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr2:234387600-234396400	Weak transcription	Primary B cells from cord blood	blood
49	chr2:234387800-234392200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:234388200-234394000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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