Variant report

Variant	rs4870905
Chromosome Location	chr8:125581871-125581872
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:125573757..125577202-chr8:125578987..125583404,3	MCF-7	breast:
2	chr8:125572972..125577628-chr8:125578200..125582090,6	MCF-7	breast:
3	chr8:125572673..125575871-chr8:125577015..125582400,6	K562	blood:
4	chr8:125577831..125580093-chr8:125580434..125583329,2	MCF-7	breast:
5	chr8:125577012..125578605-chr8:125580687..125582553,2	K562	blood:
6	chr8:125581193..125583391-chr8:125607866..125609825,2	MCF-7	breast:
7	chr8:125577321..125579071-chr8:125580874..125582837,2	MCF-7	breast:
8	chr8:125581156..125582907-chr8:125586122..125588546,3	MCF-7	breast:
9	chr8:125549873..125552042-chr8:125579435..125582392,2	MCF-7	breast:
10	chr8:125581856..125584794-chr8:125585342..125589064,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000147684	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000170873	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10090973	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10106071	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1134893	0.82[EUR][1000 genomes]
rs13260102	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13269229	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288664	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34487801	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4443647	0.84[EUR][1000 genomes]
rs4486186	0.84[EUR][1000 genomes]
rs4641047	0.84[EUR][1000 genomes]
rs4871502	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4871504	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4871505	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59751522	0.84[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	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	nsv525649	chr8:125565328-125600818	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1024804	chr8:125575803-125600950	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1025014	chr8:125578314-125600950	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4870905	TRMT12	cis	Whole Blood	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125566000-125602400	Weak transcription	Aorta	Aorta
2	chr8:125566200-125590400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:125566400-125600600	Weak transcription	NHEK	skin
4	chr8:125567000-125590200	Weak transcription	Fetal Brain Male	brain
5	chr8:125570000-125584800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr8:125570800-125605000	Weak transcription	Colon Smooth Muscle	Colon
7	chr8:125574400-125609400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr8:125574800-125590200	Weak transcription	HMEC	breast
9	chr8:125575400-125589200	Weak transcription	Esophagus	oesophagus
10	chr8:125575600-125600600	Weak transcription	Fetal Kidney	kidney
11	chr8:125575800-125589200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr8:125576400-125583200	Weak transcription	Pancreas	Pancrea
13	chr8:125576600-125583600	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr8:125576600-125591400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr8:125576800-125590200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr8:125576800-125598200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr8:125577200-125591400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr8:125577400-125582000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr8:125577400-125586600	Weak transcription	Brain Angular Gyrus	brain
20	chr8:125577400-125589800	Weak transcription	NHLF	lung
21	chr8:125577600-125582400	Strong transcription	Fetal Intestine Large	intestine
22	chr8:125577600-125586600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr8:125577600-125591600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr8:125577800-125589600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr8:125577800-125590000	Weak transcription	Osteobl	bone
26	chr8:125578000-125583600	Strong transcription	Primary B cells from peripheral blood	blood
27	chr8:125578000-125585400	Weak transcription	Right Atrium	heart
28	chr8:125578000-125585400	Weak transcription	Thymus	Thymus
29	chr8:125578000-125586600	Weak transcription	NHDF-Ad	bronchial
30	chr8:125578000-125598600	Weak transcription	Gastric	stomach
31	chr8:125578200-125583800	Strong transcription	Primary B cells from cord blood	blood
32	chr8:125578200-125586600	Weak transcription	Fetal Thymus	thymus
33	chr8:125578200-125598000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr8:125578400-125582200	Strong transcription	HepG2	liver
35	chr8:125578600-125584000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr8:125578800-125582000	Strong transcription	Fetal Muscle Trunk	muscle
37	chr8:125579000-125591400	Weak transcription	HUVEC	blood vessel
38	chr8:125579200-125582000	Weak transcription	K562	blood
39	chr8:125579200-125582400	Strong transcription	Liver	Liver
40	chr8:125579200-125586400	Weak transcription	Fetal Heart	heart
41	chr8:125579200-125590200	Weak transcription	Brain Hippocampus Middle	brain
42	chr8:125579400-125585200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr8:125579400-125586200	Weak transcription	Fetal Lung	lung
44	chr8:125579400-125589800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr8:125579400-125601600	Weak transcription	Brain Anterior Caudate	brain
46	chr8:125579600-125584200	Strong transcription	Fetal Intestine Small	intestine
47	chr8:125579600-125585600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr8:125579800-125583800	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr8:125579800-125586800	Weak transcription	Placenta	Placenta
50	chr8:125580000-125586800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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