Variant report

Variant	rs62527884
Chromosome Location	chr8:125483344-125483345
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:125482676-125483356	K562	blood:	n/a	n/a
2	POLR2A	chr8:125483112-125483476	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr8:125483289-125483487	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr8:125483039-125483397	K562	blood:	n/a	n/a
5	POLR2A	chr8:125483044-125483355	K562	blood:	n/a	n/a
6	POLR2A	chr8:125483109-125483385	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr8:125478436-125489342	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr8:125482386..125490832-chr8:125532319..125553620,55	MCF-7	breast:
2	chr8:125472502..125474578-chr8:125482316..125484294,2	K562	blood:
3	chr8:125459763..125466594-chr8:125480347..125488760,16	K562	blood:
4	chr8:125482929..125485167-chr8:125485266..125487071,3	K562	blood:
5	chr8:125459763..125466513-chr8:125482159..125488968,22	K562	blood:
6	chr8:125482257..125483957-chr8:125549259..125552139,2	K562	blood:
7	chr8:125458285..125469406-chr8:125482519..125490004,41	MCF-7	breast:

No data

Variant related genes	Relation type
RNF139	TF binding region
ENSG00000245149	Chromatin interaction
ENSG00000183665	Chromatin interaction
ENSG00000170881	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000147684	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10956184	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10956185	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11542673	0.81[AFR][1000 genomes]
rs12542260	0.81[EUR][1000 genomes]
rs12548836	0.81[EUR][1000 genomes]
rs16899649	0.81[AFR][1000 genomes]
rs4128469	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4132855	0.92[ASN][1000 genomes]
rs4512366	0.80[AMR][1000 genomes]
rs4551335	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4870898	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4870899	0.85[AFR][1000 genomes]
rs4871493	0.83[AFR][1000 genomes]
rs5004281	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62527880	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62527881	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62527882	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62527883	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62527886	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62527901	0.81[EUR][1000 genomes]
rs62527908	0.81[EUR][1000 genomes]
rs62527910	0.81[EUR][1000 genomes]
rs72713049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713064	0.83[AFR][1000 genomes]
rs72713066	0.83[AFR][1000 genomes]
rs72713074	0.83[AFR][1000 genomes]
rs7812363	0.94[ASN][1000 genomes]
rs7826104	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7834203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7836802	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7845008	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531508	chr8:125390194-125587953	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv891430	chr8:125431030-125485027	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1017848	chr8:125432689-125489052	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
4	nsv891431	chr8:125437811-125485027	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv891432	chr8:125438093-125485027	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats 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
6	nsv891433	chr8:125438093-125498547	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62527884	TRMT12	cis	Whole Blood	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125463800-125483800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr8:125464000-125484800	Weak transcription	Aorta	Aorta
3	chr8:125464000-125485000	Weak transcription	Fetal Kidney	kidney
4	chr8:125464600-125484600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr8:125464600-125485200	Weak transcription	Colonic Mucosa	Colon
6	chr8:125464600-125485800	Weak transcription	Esophagus	oesophagus
7	chr8:125464600-125486000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:125464800-125484600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr8:125464800-125484800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr8:125464800-125485400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr8:125465000-125484400	Weak transcription	NHLF	lung
12	chr8:125465000-125485400	Weak transcription	Gastric	stomach
13	chr8:125465600-125484200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr8:125465600-125484600	Weak transcription	HMEC	breast
15	chr8:125465600-125485200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr8:125466000-125485400	Weak transcription	Lung	lung
17	chr8:125466200-125484600	Weak transcription	Right Ventricle	heart
18	chr8:125466400-125484000	Weak transcription	Ovary	ovary
19	chr8:125466400-125484600	Weak transcription	A549	lung
20	chr8:125466400-125484800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr8:125466400-125484800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr8:125466600-125484000	Weak transcription	Fetal Muscle Leg	muscle
23	chr8:125467200-125484400	Weak transcription	Thymus	Thymus
24	chr8:125467200-125484600	Weak transcription	Brain Angular Gyrus	brain
25	chr8:125467200-125484600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr8:125467200-125485400	Weak transcription	Left Ventricle	heart
27	chr8:125468400-125483800	Weak transcription	NHEK	skin
28	chr8:125468400-125485200	Weak transcription	Brain Substantia Nigra	brain
29	chr8:125469800-125484000	Weak transcription	Placenta	Placenta
30	chr8:125473400-125485200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr8:125473600-125484000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr8:125475000-125483400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr8:125475400-125483600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr8:125476000-125483800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr8:125476000-125483800	Weak transcription	Brain Hippocampus Middle	brain
36	chr8:125476000-125484600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr8:125477200-125484000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr8:125477400-125483800	Weak transcription	Fetal Thymus	thymus
39	chr8:125477600-125483400	Weak transcription	Adipose Nuclei	Adipose
40	chr8:125477600-125484000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr8:125477600-125485800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr8:125478000-125484400	Weak transcription	HSMMtube	muscle
43	chr8:125478200-125484600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr8:125478200-125484600	Weak transcription	Fetal Stomach	stomach
45	chr8:125478200-125484600	Weak transcription	Osteobl	bone
46	chr8:125478400-125483800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr8:125478600-125484600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr8:125478600-125486000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr8:125478800-125484400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr8:125478800-125484400	Weak transcription	Muscle Satellite Cultured Cells	--

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